GSAS/EXPGUI use on Mac and Linux
I am interested in knowing how many people on this list are using GSAS (with or without EXPGUI) on PowerPC Macs (G4 G5 processors). If you want this hardware to be supported in future releases, please let me know (offline please!). I am also interested in hearing from people who use GSAS EXPGUI on distributions of Linux other than Redhat and/or use desktop managers other than Gnome. I'd like to know what is getting the most use and may want to get some input from you on making Linux distributions as general as possible. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Senior Physicist/Section Head for Scientific Software Advanced Photon Source 9700 S. Cass Ave, Bldg. 401/B4192work cell: 630-327-8426 Argonne National Laboratory Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov We will restore science to its rightful place, and wield technology's wonders... We will harness the sun and the winds and the soil to fuel our cars and run our factories... All this we can do. All this we will do.
Re: CIF file conversion
EXPGUI can import coordinates from a CIF (in the Phase panel) and can import diffraction data (in the Histogram panel). The represents two major steps towards creating an EXP file, but the user needs to supply plenty of other information, for example, an instrument parameter file. Brian On Feb 25, 2010, at 6:31 AM, r.m.wil...@qmul.ac.uk wrote: A quick question: does anyone know of any programs that will convert CIF data into a GSAS readable EXP file format? Brian H. Toby, Ph.D.office: 630-252-5488 Senior Physicist/Section Head for Scientific Software Advanced Photon Source 9700 S. Cass Ave, Bldg. 401/B4192work cell: 630-327-8426 Argonne National Laboratory Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov We will restore science to its rightful place, and wield technology's wonders... We will harness the sun and the winds and the soil to fuel our cars and run our factories... All this we can do. All this we will do.
Re: diffraction patterns or spectra
diffraction patterns are often referred to as diffraction spectra. But we all know that diffraction is not a spectroscopic technique. A spectrum refers to a wavelength-dispersive measurement, while CW diffraction is spatially resolved. Either diffraction pattern or diffractogram is the choice of the cognoscenti IMHO, except perhaps in the case of TOF and energy-dispersive x-ray. Brian
Re: about background substraction
On May 19, 2009, at 5:16 AM, wahyu bambang wrote: Is it alright if I substract the background and refine it a little first using another refinement software before I go through GSAS? Wahyu, While I agree with what was said in other messages and prefer to see people fit background using functions that are refined rather than do a subtraction, let me address the question above directly. The goal of a Rietveld analysis is to fit diffraction intensities using a crystallographic model, which requires that one model a whole bunch of effects (such as peak shape, background,...) that are artifacts of how the measurement was done. In the case of background, the goal is to account for the extra non-Bragg intensity that shows up in the collected data. There is nothing wrong with subtracting out any smooth arbitrary curve from the data before you fit -- as long as the uncertainties are computed from the original intensity values, not from the values after subtraction. Since this subtraction does not change the Bragg intensities or the weights, the results of the crystallographic fit are unchanged. If you do subtract a background, you are right to also do a refinement of background too. My personal opinion on this (which differs from what Rietveld-expert Dave Cox has said) is that regardless of what one does to define background manually, one should always refine a background contribution, if possible. The reason for this is that the location of the background curve indirectly determines the Uiso values for the atoms. If the background is fixed and not refined, then the uncertainty on the Uiso values is unrealistically low. For patterns having lots of overlapped peaks at high angles, this location is no better determined by eye than by refinement and in some cases there is no unique solution. When this happens, the inability of the refinement to find a minimum (or a minimum with reasonable Uiso values), lets you see that the data are not sufficient to determine Uiso and background -- a very useful thing to know. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Senior Physicist/Materials Characterization Group Leader Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov We will restore science to its rightful place, and wield technology's wonders... We will harness the sun and the winds and the soil to fuel our cars and run our factories... All this we can do. All this we will do.
Re: UVW
Dear all, According to Caglioti relation, the dimensions of U,V,W are as (angle)^2. So, should we treat their units as (centidegree) ^2 in GSAS profile menu? Thanking all Yes. (FYI, this is in the GSAS manual). Brian H. Toby, Ph.D.office: 630-252-5488 Senior Physicist/Materials Characterization Group Leader Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov We will restore science to its rightful place, and wield technology's wonders... We will harness the sun and the winds and the soil to fuel our cars and run our factories... All this we can do. All this we will do.
Re: GSAS data formats
I do not recommend using this format. Better choices are the ESD variant on this, where numbers are alternated intensity, esd, intensity... (and there are a lot more digits for each number) or the FXYE format, which has angle, intensity, and optionally esd, one entry per line in free format. My recollection on this is that YO is the total number of counts, so the normalized Intensity = YO/n and the error on that is SQRT(YO)/n. The idea being that not all measurements are made with the same number of detectors. Brian On Mar 16, 2009, at 12:02 AM, matthew.row...@csiro.au wrote: Hi all I'm going over the GSAS data format (by reading the manual), trying to figure out how it works, and I've come up with a couple of questions: 1) In a STD data set, the manual says that NCTR is the number of counters and YO is the n number of counts per counter. So, for a single data point 3 3452, is the total counts =3*3452? What is the error? Sqrt(3*3452), 3*sqrt(3452) or sqrt(3452/3)? 2) What is the data format for type = ALT? The manual (http:// www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/ GSASManual.pdf) doesn't say... Cheers Matthew Matthew Rowles CSIRO Minerals Box 312 Clayton South, Victoria AUSTRALIA 3169 Ph: +61 3 9545 8892 Fax: +61 3 9562 8919 (site) Email: matthew.row...@csiro.au Brian H. Toby, Ph.D.office: 630-252-5488 Senior Physicist/Materials Characterization Group Leader Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov We will restore science to its rightful place, and wield technology's wonders... We will harness the sun and the winds and the soil to fuel our cars and run our factories... All this we can do. All this we will do.
Re: Rietveld: U,V,W
What is the correct procedure for refining U,V,W? It is my understanding that those parameters are a function of instrument geometry. Does one use a standard material to determine U,V,W and then fix their values for the instrument you're using?or do the values of U,V,W change depending on the sample being examined? If so, why do the values change? The GSAS manual covers the latter part of you questions pretty well, though perhaps indirectly. In theory, U and W should be instrumental constants that will not change with sample, while V can have both an instrumental and a residual stress component. However, this assumes that one also refines a crystallite size parameter, P when needed, which many people (myself included) do not. In that case, U, V W will all change to compensate for crystallite broadening. I do recommend using a standard with good sharp peaks (SRM LaB6 is the ideal, though there are likely to be many other oxides handy that work reasonably.) If you can't get a good fit to your standard, then you do not want to advance to an unknown until you understand the problems with your instrument/technique. Where possible, I try to start a refinement with values that are close to correct for U, V W (+ X Y where significant) and put off refining them until late in the refinement, when they tend to be pretty stabile. Initially, I usually refine U, V W together and then refine X and then Y solo and then finally in combinations until everything is refined together. Look for parameters that are refining to zero and turn them off, since GSAS does not deal with that very well. Also look at the widths vs 2theta (widplt) to see if the functions are reasonable. The routine in CMPR for fitting U, V W values to a set of peak widths has been useful for me where I don't have good calibration information for an instrument. FullProf might be a bit more stable, but I think the process there is about the same. (BTW, if anyone works out how to convert GSAS profile terms to ones used in FullProf, I'd be interested to get those relationships into CMPR; I am not sure if the scaling is only between centidegrees**2 and degrees**2.) Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: GSAS bond angle reconstraints
When setting up a bond angle soft constraint in GSAS, one needs to input the atomic sequence numbers for the three atoms. However, if two of the three atoms are the same and have the equivalent positions (e.g., Si-O-Si), the two atoms have the same sequence number from the atomic list. GSAS seems to only accept three different atomic sequence numbers. What should be done? The angle constraints (as opposed to the distance constraints) do not allow symmetry to be used. Thus the atoms must be distinct and must be adjacent in the asymmetric unit. There is no easy way to constrain an angle that involves the same atom twice. This might work, however: I have considered the idea of putting dummy atoms (with occupancy zero) into the asymmetric unit and then constrain the dummy atom to refine along with the real atom (getting the symmetry directions correct). Then one can use the dummy atom in the constraint. This should work, but I have not tried it. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: unit cell size limitation in GSAS?
I have used GSAS with unit cells as large as 25 A on a side. I do not believe there is any limitation in cell dimensions. I would guess that this is a user error (the most common reason for an error from POWPREF is an error from the previous cycle of GENLES). If you really believe that you have encountered a bug, report it to Bob with enough information so he can track it down. Brian On Nov 12, 2008, at 2:10 AM, Jae-Ho Chung wrote: Dear all, I am trying to use GSAS to do Rietveld refinement of the pulsed spallation neutron diffraction data. I just found that an error should occur in powpref when I tried to use unit cells of the size approximately 16.5 Angstrom or larger. Unfortunately, the unit cell I need to use slightly larger than 17 Angstrom. Is this an intrinsic limitation of GSAS? Is there a way to get around it? Thank you very much. Jae-Ho *** Jae-Ho Chung, Assistant Professor Department of Physics, Korea University Anam-dong 5, Seongbook-gu Seoul 136-713, Rep. of Korea tel.) +82-2-3290-3116 fax.) +82-2-927-3292 web.) http://scattering.korea.ac.kr *** Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: confusion about some GSAS parameters
On Aug 7, 2008, at 12:02 PM, [EMAIL PROTECTED] wrote: So, for the case of a brag brenteno diffractometer without any monochromator, will the value for POLA should be fixed to zero?? There are two GSAS polarization models (read the manual!), but my recollection is that for IPOLA=0, POLA should be 0.5 when you have no monochromator or analyzer. Brian
Re: 1/Yo**2 weighting scheme in Rietveld refinement
On Mar 14, 2008, at 5:41 AM, Franz Werner wrote: w=1/Yo**2 [weighting] is proposed (By using the new weighting scheme, the accuracy of positional parameters of the test sample was significantly improved relative to the weight function 1/Yo, which weights the medium and strong intensities more heavily, is in accordance with statistical theory and gives a better overall fit between the observed and calculated powder patterns.). I'll give my stock comment in response. For fitting of data with only statistical errors, you obtain the smallest uncertainties on the fit parameters when weighting is w = sigma**-2. This requires that you know the experimental uncertainties (no image plates or other non- quanta counting detectors). Further, if your data have only statistical errors, then chi**2 ~= 1. Any other weighting scheme is effectively throwing away data. In cases where there are non-statistical error sources, then you do gain by down-weighting the data most effected by systematic errors. However, be aware that the systematic error you are choosing to reject could be trying to tell you that really would want to know: e.g. the model you are using is incomplete or even wrong. If you have reason to believe that your measurements are inaccurate in a particular way (for example uncorrected deadtime, sample roughness, or funky peak shapes, etc) it might make sense to change the weighting function, but I personally don't think there is a generic source of error in all diffraction measurements that would make it appropriate to use the same weighting change for all types of data and materials. Brian
Re: Graphic superposition of crystal structures
On Jan 17, 2008, at 4:04 PM, Franz Werner wrote: Does anyone know a free program capable of overlaying crystal structures? The DRAWxtl program has some capabilities for this -- see the frame command. http://home.att.net/~larry.finger/drawxtl/ Brian
Re: Crystallography/MS Word Question: 3 bar
On Jan 14, 2008, at 4:36 AM, Holger Kohlmann wrote: try the font Arial Overlined, but make sure to install it on any computer you use. I once gave a talk with the title 1 bar, written in Arial Overlined. Of course, the computer in the lecture hall did not have that font, which turned the title into 1. Not very clever, if you want to give a talk on inversion symmetry, ... I think there is an option to embed fonts into a powerpoint document that would help with the latter situation, but has some other drawbacks with respect to editing or such... Thanks to all for very useful comments. Brian
Crystallography/MS Word Question: 3 bar
I have heard that there are several ways to create a 3 with an over- bar symbol (as would be used for space group R -3 c, for example) in Micro$oft Word, but none are convenient. I know how to do this with the equation editor. Can anyone contribute any better choices? Brian
Re: question about PowPref, GSAS
Choice of space group origin will affect the computation of intensities but not which reflections are included in the pattern, so that is not the problem. The fact that the 222 reflection shows up in reflist makes it seem likely to me that you do not have the space group input correctly. Hi Brian, Thought the (222) reflection was missing in silicon due to the site symmetry only? Does not look like a space group absence at: Yes indeed, quick answer, but wrong. The 222 reflection is zero in intensity, but not is not absent due to space group symmetry. The problem was indeed one of origin choice, not symmetry input. And I even missed a chance to flog the Convert Origin 1 - 2 button hidden in EXPGUI. Brian
Re: inclusion of organic template with GSAS
You may be lucky enough that bond distance and angle constraints will be sufficient for your purposes. Do not be afraid to weight them very highly, so that they will have significant leverage on the refinement. If your cation is complex, the constraints may not be enough to keep the geometry reasonable. In that case, rigid bodies are the way to go, but they can be quite complex to set up, particularly if you want to allow some internal degrees of freedom. Here are links to two tutorials on rigid bodies, from Robert Dinnebier and Ian Swainson: http://www.uni-bayreuth.de/departments/crystal/rietveld/rigid_bodies.pdf http://www.ccp14.ac.uk/ccp/web-mirrors/ian-swainson/ fireside_fuide_to_rigid_bodies.pdf Brian On Dec 11, 2007, at 3:19 PM, Ramadas Sunil Pophale wrote: Dear friends, I am new to the community and had a question for GSAS users. I have a powder diffraction data for a zeolite + template (organic molecule) system. I would like to know the best way to represent the molecule for refinement purposes. I currently include it as part of a phase along with the Si and O atoms and set soft constraints on the bond lengths. I wonder if this approach is good enough or should I try the rigid unit option (which does not look trivial, any good link discussing this option?) Thanks for your help. Regards, Ramdas Pophale. Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: GSAS on Windows Vista
On Nov 27, 2007, at 7:48 AM, Davide Levy wrote: I am changing PC and I would like to know if there are problem to run GSAS-EXPGUI with Windows Vista. I have heard reports of problems with running the self-installer. This probably requires use of a sys admin account on Vista (and probably on XP, too, depending on security settings). If you do use the self-installer, be sure to upgrade with the latest GSASKIT, as there have been many updates since the last time I put together a self-installer. Brian
Re: Difference Fourier Map/GSAS
Are you sure that you are not looking at parts of the unit cell that are symmetry-equivalent to the peaks found in FORSRH? You can also use the FORPLOT program to make 2-D plots to confirm that what FOX (or equivalently DRAWxtl) shows agrees with the internal GSAS representation. Brian On Nov 22, 2007, at 8:19 AM, Telepeni Irvin wrote: Hi Vincent, I meant: (2) that the positions of your Fourier difference peaks are not the ones you see by looking a the 3D Fourier difference map (exported from gsas) in Fox ? I guess I am using the latest version of both since I reinstalled everything just to make I was missing something important. Even when I put D where GSAS thinks it should be (and where I hope it should be as well), then it turns out that this site or those sites are hardly occupied (and they are those to be supposingly where the scattering is from). Cheers Irvin This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: Difference Fourier Map/GSAS
On Nov 22, 2007, at 11:30 AM, Telepeni Irvin wrote: Thanks for your reply, that must be the explanation, but I am not quite sure of how to filter these sites from those of interest (since I dont know where they are)? I could just try all of them but I am sure that's not the ideal method. When you compute a Fourier map in GSAS, it is best to compute it over only the minimum volume needed to allow computation of the entire unit cell (aka asymmetric unit). If you do that FORSRH will not find multiple symmetry-related peaks. My experience is that only the first few Fourier peaks are meaningful in a powder difference Fourier, so I will put trial atoms at the first few positions found in a map -- if they make chemical sense (you might want to save then and then use DISAGL to look at distances and angles to test that). My first step after including them is to refine occupancies (with fixed positions and Uisos) of the trial atoms to find if putting scattering density at the site actually improves the model. If the occupancy refines very small, then it is hard to believe in the site. Irvin, your previous questions implied one of two things might be true: that FORSRH is not giving you peaks where the map is showing positive density or that you do not see peaks in the map when plotted in FOX corresponding to the peak locations found in FORSRH. If either is true, you may have found a bug that needs to be documented if it will be tracked down and fixed. With luck, the software is fine. Brian
Re: Kapton capillaries
Could someone please suggest a source for purchasing kapton capillaries? A search on the internet drew a blank. Try polyimide rather than kapton. We have used MicroLumen as a vendor: http://www.microlumen.com/ Brian
Re: Instrumental parameter file
How do I obtain the instrumental parameter file for the powder diffractometer (Siemens) I am using? Alice, At the risk of self-promotion, one way to start is covered in a canned talk. See topic #1 on this web page: http://www.aps.anl.gov/Xray_Science_Division/ Powder_Diffraction_Crystallography/EXPGUItricks.html Visit starbucks first; the talks can be pretty dull. soapbox Convince everyone in your group starting with your advisor (better yet, department) to ask your library to subscribe to ICSD. We do. Cost is very reasonable compared to most journal subscriptions. At worst, your group should be able to manage the cost of a single-seat license; cost compares favorably to the student-discounted price for many commonly used software packages. /soapbox Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: Is it possible in GSAS to control the value of certain parameters in a
Re: Is it possible in GSAS to control the value of certain parameters in a... For example, Uiso0, 0F1, etc No. Nor would you want to do this. When Uiso or Occupancy refine to non-physical numbers (particularly with neutron data) there is a implicit message that your model is not fitting your data properly or you are using too many parameters. You want to pay attention to this, not sweep it under the rug by adding a constraint to the fit to hide the problem. There are occasions when Uiso values cannot be modeled in Rietveld. In these cases one should constrain the parameter by not refining it (and explaining why this was needed in the associated publication.) More common is to group Uiso parameters or fix background parameters. One may want to constrain the sum of occupancies, but I see no reason to ever constrain F 0. Brian
[Fwd: [ccp4bb] Nature policy update regarding source code]
Begin forwarded message: From what I have read on Nature Methods decision then if the journals of J. Applied Cryst and Acta Cryst were to go down the same path then 2000 plus users of TOPAS and TOPAS-Academic would be without a means of reading peer reviewed articles on the algorithms used by those programs. This would be a tragedy... I think that people are misreading the intent of the editorial. From the abstract: Software that is custom-developed as part of novel methods is as important for the method's implementation as reagents and protocols. Such software, or the underlying algorithms, must be made available to readers upon publication. Note that TOPAS is available to Nature Method readers... one only has to buy it, so no problem here. The problem is really when a scientific result is obtained with software that is both unique and not distributed. How could cold-fusion, polywater etc be debunked if one has to know the secret handshake to know enough details to duplicate the work. I personally feel that open source software is usually in the best interests of scientific methods development. I would be uncomfortable if the only method available to me to check that a structural model matches data were a single undisclosed code (such as GSAS or TOPAS). However one has a wealth of programs that can be used to verify that a model matches the observed data. In worst case, I could pull out a calculator and grind out some structure factors. There may be some improvements in the algorithms, but the fundamental equations are all well understood here. Access to code improves science, IMHO. When people can read through code, errors are spotted. Access to code allows a motivated scientist to develop a new method by building on an existing one rather than starting from scratch, where the latter can be a huge hurdle. Perhaps the argument is less acute, as few scientists are prepared to code or even modify programs. However, I don't see the intent of the editorial to force that model on anyone. Brian
Re: Exporting GSAS powplot data
You can also export from liveplot in a few different formats including .csv for use in a spreadsheet. I am open to suggestions on other ASCII formats for data export -- but be prepared to research that format so you can tell me exactly what needs to be written. Brian On Mar 15, 2007, at 8:21 AM, Duncan, Jo wrote: Hello RR people. How can I extract the information in powplot (in GSAS) for use in another package e.g. excel ? i.e. how can I get the x and y values of Refined pattern, histogram and residual? Many thanks Jo Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Announcement: GSAS-II Workshop May 10-11, 2007
GSAS-II Rietveld Software Development Workshop: May 10 11 Argonne National Laboratory Building 360, room A224 C232 A small workshop is being organized at Argonne National Laboratory on May 10 11 to discuss a potential future comprehensive, extensible and adaptable crystallographic software package. The speaker list is incomplete at this time, but is expected to include Alan Coehlo, Ralf Grosse-Kunstleve, Bill David, Vincent Favre-Nicolin, Simon Billinge, Bob Von Dreele and others. We see development of such a code as a long-term project that would be carried out in parallel with the continued maintenance of GSAS EXPGUI, until such time as the new code can replace the existing ones. The need for such a code is driven by a need to expand the scope of crystallographic data analysis to also utilize data from any other experimental method that can be simulated from an atomistic model and likewise incorporate theoretical and empirical models. The workshop goals are to understand limitations in existing codes, to envision the science that can be done with an extensible and adaptable package, and to discuss design strategies for GSAS-II. Participants will develop a report on our findings. Organizers are Simon Billinge, Alan Coehlo, Jim Richardson, Brian Toby, and Bob Von Dreele with help from Juan Rodriguez-Carvajal. We have very limited funding and seating space, but welcome contact from scientists interested in attending. Please send e-mail to the workshop secretary, [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] (do not reply to this message!); let us know in a paragraph or two what your interests would be in this area and, if appropriate, what you would like to present. Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Powder Diffraction In Q-Space: plotting CIFs
On Feb 22, 2007, at 4:54 AM, Alan Hewat wrote: Now this sounds interesting. Certainly the raw data should be archived and people could then plot it as they wish. But are there examples of interactive plotting applications embedded in powderCIF files, and what language might they use ? I would like to see a profile plotting package in Java or some other really portable language that would read in CIF files and plot calculated-observed patterns like Jmol now plots structures. Alan. A large part of my motivation for the decade I invested in pdCIF was that postage stamp size plots do not allow one to really understand the quality of a Rietveld analysis fit. The pdCIFplot application will plot in Q, provided the software has the information needed to convert the supplied units (it does not know how to convert energy or time-of-flight, but does fine with 2theta or d-space). It can be used to plot intensity/s.u. -- although that is a rather clumsy thing to set up in the custom plot menu. The source code (Tcl/Tk) is distributed, so if anyone would like to add new features -- I'd love to get them. I should also plug my work by noting that pdCIFplot also allows plotting of Bill David's reduced chi squared or (obs-calc)/ sigma and will show the relationship between the intensity scale will also allow one to look at the relationship between the reported intensity scale and the equivalent value as counts. (See www.ncnr.nist.gov/xtal or CCP14 for ciftools downloads; N.B. the pdCIFplot paper is open access: http://journals.iucr.org/j/issues/ 2003/05/00/aj0008/aj0008.pdf) pdCIFplot is not an application embedded in a user's CIF (in fact DDL3 embeds apps in the dictionary not in the files), nor is it embedded in a web browser -- though I think that could be possible. Alan, perhaps you might be able to figure out how to configure firefox to launch pdCIFplot when it encounters a .CIF file on various platforms? There is an open question of how pdCIF will get updated from DDL1 to DDL3. The pdDMG needs a new chair willing to take pdCIF into the next decade. I think I have paid my dues. I will not make any (more?) enemies by suggesting suitable candidates. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: Powder Diffraction In Q-Space
I have always preferred to see data plotted in units of Q (though Q^2 or Q^3 makes sense from a perspective of spreading peaks.) Two-theta made sense only when everyone used CuK alpha (which was never true). Personally, I would be glad to never see another plot of intensity vs. d-space. On Feb 21, 2007, at 10:29 AM, Von Dreele, Robert B. wrote: OK, I did play about display some Q-space (Q=2pi/d) plots in GSAS. It will be an option in the next release. It has been an option in LIVEPLOT (EXPGUI) for many years. (Sorry, could not resist.) LIVEPLOT output can be exported WYSIWYG to XMGRACE or as a .csv file. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Marija): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: scale factor
Intensitiywise, Most variables can be classified as withdrawing or adding. In the former group, we can find the thermal parameters, the profile coefficients and the scale factor; Would it be a valid strategy to turn the scale factor flag off at some point to make sure positive thermal paramenters are obtained? This is not how I would think about the fitting process. A large Debye-Waller parameter removes intensity from the high Q part of a pattern. Coupled with the idea that we do not know the scale factor and have to fit it also, Uiso values effectively shift intensity between the high and low Q sections of the pattern. This does not create a problem, when reflections are well separated across the pattern, so that the background is well defined. However, in many cases, one wants to use data where reflections clump together (typically at high Q) so that the background location is not uniquely determined across the entire data set. In this case, one can find a range of fits that produce more or less equivalent results with a range of background, profile, Uiso and scale factor values. Smaller than expected Uiso values for all atoms commonly result from this. (This will not produce a negative Uiso for a single atom where all other values are in a reasonable range.) Under such circumstances, where the data do not allow all parameters to be fit independently, I will typically fix the background values and then note this in the paper, but I will never fix the scale factor, since that is completely arbitrary in almost all experiments. Brian Brian H. Toby, Ph.D.office: 630-252-5488 Materials Characterization Group Leader, Advanced Photon Source 9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Kristy): 630-252-5453 Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: GSAS: Linux install
I do not know anything about Ark in SUSE but there are general Linux instructions: http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_Unix_readme.htmlThe GUI is EXPGUI; the command line script is file .../gsas/gsas. Both are present in the gsas+expgui.tar.gz file, only GSAS in the gsaskit.tar.gz file.There is only a 32-bit version and I am no longer preparing RPMs. For newer SUSE installations, expect to install some compatibility packages to run the distributed binaries as they require shared libraries that are not included in the base install.BrianOn Oct 25, 2006, at 5:05 AM, [EMAIL PROTECTED] wrote:Dear all,I can't unpack GSAS using the command line. It states something along thelines of the file not being the correct format?I am using SUSE 10.0 x86_64 and if I use Ark that comes with SUSE it unpacksno problems - I think. When I run the script all I get is the command line -is there a GUI front?I can not find the ./cshrc file either? Is that particular to Red Hat or am Imissing something?Is there an uptodate binary or rpm version at all and 64 bit?Kind regardsWilliam Bisson Brian H. Toby, Ph.D. office: 630-252-5488Materials Characterization Group Leader, Advanced Photon Source9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Kristy): 630-252-5453Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: Dummy histograms
RAWPLOT plots diffraction data not results from fits. You want to use POWPLOT to plot the results. What you are trying to do below is plot from an instrument parameter file -- which contains no data.BrinOn Sep 14, 2006, at 2:30 PM, Will Bisson wrote:Dear all,I am having issues trying to get RAWPLOT to plot a dummy histogram. I created from scratch an exp file, input a dummy histogram using a parameter file for the D20 at the ILL. I have input all my atoms. The scale factor is set to large (1) and all refinement flags are off.For some reason every time I want to generate a powder pattern for a particular wavelength I end up with this error. It is irrelevant what scan numbers are input, on the second time of asking for a scan number it crashes?Error.GIF I will be grateful if someone can tell me the best method to display a dummy histogram.Many thanksWilliam-- William BissonDavy Faraday Research Laboratory The Royal Institution of Great Britain 21 Albemarle Street London W1S 4BS Tel: +44 (0)20 7670 2977 (Direct) Tel: +44 (0)20 7409 2992 (Switchboard) Fax +44 (0)20 7670 2958 Http://www.ri.ac.uk/DFRL/ The RI is a registered charity (number 227938) Brian H. Toby, Ph.D. office: 630-252-5488Materials Characterization Group Leader, Advanced Photon Source9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Kristy): 630-252-5453Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: GSAS ESD/STD conversion
I am trying to convert a GSAS ESD file to a GSAS STD file There is a problem here that cannot be solved by any conversion program. One typically uses the GSAS ESD format for data that are scaled in some fashion, so that estimated errors (s.u.'s) on the intensity values are not the square roots of the intensity values. Stripping out the s.u.'s means that your statistical uncertainties ( chi**2) are now potentially meaningless and that some parts of your pattern could be over/under-weighted with respect to other parts. I think that CMPR can plot the ratio of sqrt(I)/sigma (which should be 1 for all points, if you have intensities as counts). Doing that will give you an idea of what the optimum multiplication factor would be and how bad the idea of dropping s.u.'s will be for your data (how the scaling deviations from a constant) -- if you are going to ignore my cautions.BTW, I would be surprised if FullProf does not have a way to input intensities with uncertainties rather than assuming intensities are counts.Brian Brian H. Toby, Ph.D. office: 630-252-5488Materials Characterization Group Leader, Advanced Photon Source9700 S. Cass Ave, Bldg. 433/D003 work cell: 630-327-8426 Argonne National Laboratory secretary (Kristy): 630-252-5453Argonne, IL 60439-4856 e-mail: brian dot toby at anl dot gov
Re: Converting .RAW file to correct format in GSAS
On Jun 20, 2006, at 10:37 AM, [EMAIL PROTECTED] wrote:I am trying to import a histogram which is in the .RAW format into GSAS. I am having problems converting this into the correct format for GSAS. The error says permission denied. How can I solve this problem and/or get a permission to convert such files. Thankyou. "Permission denied" sounds like a computer setup problem. Do you have write access to the directory where you are trying to work? I suggest creating a new directory and copy the files you are using to that location and check the permissions on those files. Brian
Re: CIFs for powder diffraction/Software testing
Brian H. Toby wrote: At present, to my knowledge, there is exactly one program that can be used to read plot powder diffraction data from these CIFs: pdCIFplot This turns out to be wrong. CMPR can also do this (http://www.ncnr.nist.gov/xtal/software/cmpr/). My apologies to the author of that program. Brian
Re: Rf values in GSAS
Run program rfactor. You get the choice of computing on F**2 or F. Brian Does anyone know any way of extracting Rf values from a GSAS powder data refinement? I can't find any mention of it in the manual.
Re: Rigid body constraints on perovskite structured materials
As per Brian Toby's advice on using strong restraints instead of rigid bodies. My advice was to use restraints (soft constraints) together with rigid bodies, although, restraints on both bond distances and angles can be an alternate strategy. Brian
Re: A question about stacking faults
I would suggest you look into the work of Mike Treacy et al. and in particular his DIFFaX program (check ccp14 for links.) The effects of stacking faults on diffraction patterns can be quite complex and are not simulated through use of models that contain long range symmetry. Brian ling yang wrote: Are there anybody experienced in stacking faults? Please help me! Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal
Windows GSAS+EXPGUI *now* updated
Friends, My previous e-mail stated that the combined GSAS/EXPGUI distribution had been updated for all four supported platforms. This was wrong. I just discovered that the updated Windows version did not get onto the webserver until a few minutes ago (my fault). My sincere apologies to all of you who downloaded non-updated file based on my previous message. (I do note that apparently no one reads the installation screens -- since they read Version of May 2004... ;-) ] The URL for the updated file is: ftp://ftp.ncnr.nist.gov/pub/cryst/gsas/gsas+expgui.exe The installer intro pages should read versions of Sept. 2004, if you have the right file. If you will grab this from a CCP14 mirror, check the file date before you download. Mirror updates can take a day. Again, sorry Brian
Updates to GSAS+EXPGUI
Friends, A new and updated combined release of GSAS EXPGUI is now available on all platforms (Windows http://www.ncnr.nist.gov/xtal/software/expgui/expgui_Win_readme.html, LINUX/SGI http://www.ncnr.nist.gov/xtal/software/expgui/expgui_Unix_readme.html, or Mac OS X http://www.ncnr.nist.gov/xtal/software/expgui/osx.html). For details on what is new, ask someone on the EXPGUI mailing list to forward you the message about that release or see the EXPGUI Recent Planned Improvements http://www.ncnr.nist.gov/xtal/software/expgui/wishlist.html web page. Brian
Re: Ca, Sr-chabazite
Can someone please send me the atomic coordinates of Ca and Sr chabazite data. The IZA (http://www.iza-structure.org/databases/) is a good place to look for info on zeolite structures. If nothing else you can find literature references for CHA structures. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal
Re: Conversion software available?
This can also be done with the CMPR program (see CCP14 site or link below). CMPR runs in Windows, OS X and unix. Note that you think carfully about how you would process data after wavelength conversion, as many computations will not give correct results. As one example, anomolous dispersion (f' f) will not be computed correctly. Brian I am looking for software that can convert the x-ray diffraction data of one radiation source to the other. Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal
Re: Rietveld refinement and PDF refinement ?
Alan, But if you refine the full data with the same model, can there really be any fundamental difference, if in one case you simply do a Fourier transform to real space ? in Rietveld refinement we throw away the non-Bragg peak data, where-as with PDF all scattering is included. It is funny to switch roles and argue this from your side w/r to the papers we each published on the disorder in the Tl2Ba2CaC2O8 superconductor in the 80's (you worked on the problem with pretty much traditional methods while Takeshi Egami, Wojtek Dmowski and I developed methods for modeling the PDFs of crystals -- and we did come up with results in pretty good agreement). I would argue that the Bragg diffuse scattering both reflect the average instantaneous atomic structure. In the case where PDF shows split sites and the Rietveld gives the high symmetry site, this is really a failure of our crystallographic modeling techniques, as the split model should really do a better job with the Bragg-only data, too. As Paolo pointed out before I could finish this e-mail, the place where the PDF is different from crystallographic results is that the former will reflect correlation in interatomic distances. The other idea you raise, could one use the entire range of Q, up to 25 A-1 or even 50 A-1 in Rietveld to me raises a more profound question. In conventional use, the answer is probably no -- adding the gentle wiggles at high Q to a refinement provides almost nothing new. The reason for this is that Rietveld treats the background at high Q is an adjustable parameter. Thus, there are no termination errors in Rietveld, but the leverage of the high-Q data w/r to the ADPs is nearly zero once the peaks start to get quite broad due to extensive superposition -- where the computer (or user) draws the background curve is arbitrary. In total scattering the background is measured experimentally and fixed. Perhaps in the quest for fundamental parameters, someone should develop a Rietveld code that uses additional background empty container scans (as is done to obtain the PDF) so that instrumental background is derived rather than fit in Rietveld. Then we could then have ADPs on an true absolute scale (something more important IMHO than relating every blip in peak shape to something intrinsic to the instrument or sample.) Finally, in the shameless self-promotion department. Simon and I just published a paper in Acta A on error analysis with models fit to PDFs. The results: s.u. from models fit to PDFs (if done right) are equivalent to those of Rietveld (for the same reasons why Bill David et al can do a Pawley fit and then get the same esd's by fitting to the extracted I's). However, s.u.'s from a PDF model fit values should be smaller, since it typically uses more data. Brian
Re: PDF-4
I suspect that the ICDD-JCPDS PDF-4 format is not public, but I am not certain on this. John Faber at the ICDD is the person to contact. Certainly the ICDD wants to keep tighter control on the PDF-4, since that is leased year-by-year, so I imagine they would not want to see it be open. There is commercial and ICDD windows software for the PDF-4, but I am not aware of anything else. As far as non-windows software for the ICDD PDF-2 database goes, there is a fair amount of older VAX code that could be ported, with varying degrees of effort needed, but the only open and working code that I am aware of is the PDF-2 search/display software now included in the CMPR program (see link below), which runs in Linux, Mac (OS X), SGI ( probably all other unixes) and, oh yes, Windows. Brian Friedrich W. Karau wrote: Dear colleagues, does someone know, if the database format of the the new PDF-4 Database, is public, and if there is a database access tool for LINUX/UNIX systems? thank you in advance, Friedrich -- Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal
Re: EXPGUI updates?
There will not be any updates before August and quite possibly September for gsas+expgui. You can load the gsaskit on top of the gsas+expgui installation to update, provided you are careful to put the files in the same locations. Brian Marcelo J.G. Silva wrote: Dear all, Do you know if there is already a version of gsas+expgui.exe up to date with the newest version of GSAS from 26-Jun-2004 18:46 7.5M (gsaskit.exe http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/windows/gsaskit.exe) ? Thanks, Marcelo == Marcelo J. Gomes da Silva - [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] PhD Candidate Department of Mechanical and Nuclear Engineering 127 Reber Building, University Park, PA 16802 U.S.A. The Pennsylvania State University http://www.personal.psu.edu/mjg301/ == -- Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8563 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8563 http://www.ncnr.nist.gov/xtal
Re: Next Endeavour version without Hofmann potential
I have to agree with Vincent that I find aspects of CCDC's apparent actions troubling and warrant discussion even if all parties reach a happy agreement behind closed doors. If the CCDC claims partial ownership of everything derived from their database then how far does that go? Can they prevent someone from publishing an average bond distance mined from 10,000 structures? Do they require that the entire staff of the CCDC be included as coauthors? Alan is correct that there is much that we do not know: What information has Dr. Hoffmann has supplied only to Crystal Impact and what information is in the public domain? Since much is unclear, I will offer one possible argument on the CCDC's behalf. Academic researchers are given access to the CSD (and other) databases for academic (public) research at rates considerably reduced from that of commercial research. If someone makes a discovery from these academic facilities but rather than disclose it in the open literature, instead decides to use that information for private gain (either for the researcher or the employer's institution) then from my perspective this academic researcher/institution is cheating by paying academic rates, but performing commercial research. (I am not suggesting that I know this to be the case here). The CCDC is a valuable resource to our scientific community. The CCDC should take all steps needed to protect their intellectual property -- which is their compilation of data (note anyone can compile their own data collection from the literature by simply typing in all the coordinates again), plus the wealth of tools they have built over the decades, as well as the comments and corrections they have created and include in their data collection. I think it reasonable that the CCDC forge agreements with organizations that would mine their data collection for profit. If on the other hand, the CCDC works to prevent the open publication of research results that derive from their data collection, or uses their size to prevent companies from producing software that competes with their own products, then I think they can no longer claim to be a non-profit organization dedicated to the advancement of chemistry and crystallography for the public benefit... (I am also not suggesting that I know this to be the case here). What exactly is the case here? I don't claim to know. I would hope that Dr. Hoffmann will publish all of his results from use of the CSD. At that point I would hope that the CCDC would not feel that algorithms or software that implements this public information is their intellectual property, unless developed within the CCDC. I will wait quietly and see what we learn over the months to come. Brian
CIF files input to GSAS
You can import unit cells coordinates from CIFs into GSAS via EXPGUI. I think I wrote a routine to do the same from PowderCell .CEL files, but I don't remember for sure. There should be an example that shows how this is done somewhere. Check my alumina tutorial or look on CCP14. Brian Von Dreele, Robert B. wrote: Dear Marcelo ( others), GSAS should do texture (sph. harmonics) with film data (or image plate) powder data. Image needs to be divided up in to 'pie' sections integrated to give a sequence of patterns about the azimuth. The read them as separate histograms in GSAS give each the appropriate azimuth angle (set that in histogram editing). Azimuthal angle is right handed looking away from source zero is in right side horizontal facing the source. Hope that's clear. GSAS will not read cif files. Bob Von Dreele From: Marcelo J.G. Silva [mailto:[EMAIL PROTECTED] Sent: Tue 5/18/2004 2:08 PM To: [EMAIL PROTECTED] Greetings all, I have to questions (to make it simple); any help is welcome, please. I am trying to perform some refinement with Rietveld using GSAS and I am not sure if by loading the CIF or the CEL files already takes that into account. Can anyone help me, please? I try to enter manually the values in EXPGUI but really am not sure which way is the correct. Thank you. I am also having a hard time fitting synchrotron data from a film (highly textured) and sometimes I wonder if it is possible. If someone can give a hint, I would really appreciate it, even if the hint is: not possible!!! Marcelo == Marcelo J. Gomes da Silva - [EMAIL PROTECTED] PhD Candidate Department of Mechanical and Nuclear Engineering 127 Reber Building, University Park, PA 16802 U.S.A. The Pennsylvania State University http://www.personal.psu.edu/mjg301/ == -- Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: Fixing parameters in GSAS
Nope -- EXPGUI does not handle the Fix option (yet). Brian Peter Zavalij wrote: The easiest way is to use EXPGUI graphic user interface by Brian Toby. Peter Zavalij -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Thursday, April 22, 2004 5:05 AM To: [EMAIL PROTECTED] Dear all Rietvalders, Can anyone know how to delete the holding parameter (F option under the atomic parameter menu in GSAS)? since the program does not allow me to remove them even after pressing D for those variables? They are still there anyway. many thanks stephen
no new EXPGUI yet
Dr. K. Selvaraj wrote: Dear Brian Is there a latest version of EXPGUI ? Thanks I am trying to find some free time to track down a few EXPGUI bugs. Once they are caught, I'll put together a new release of EXPGUI combined with the latest version of GSAS for windows. After that, then Mac OSX, Linux and SGI releases, probably in that order. With everything else I am trying to get done, it will be at least a week before I get the windows version out. Brian
Re: GSAS information (anisotropic microstrain)
My advice on this question is that one should not use this approach. The Stephens formalism, coded in profile type 4, is better founded by theory. See the GSAS manual and reference to Peter Stephen's J. Appl. Cryst paper from a few years back. Brian Christophe Chabanier wrote: Hello everybody, i have a question about the GSAS software. Indeed, i would like to know what are exactly the L11, L22, L33L23 parameters. I saw that these parameters represent the anisotropic microstrain in material. Moreover, there is an empirical expression which uses these parameters as following : Gamma(L) = L11*h^2 + L22*k^2 + L33*l^2 + 2*L12*hk + 2*L13*hl + 2*L23*kl I would like to know and understand the physical representation of these parameters and this expression. Thanks in advance Christophe Chabanier INRS-Énergie, Matériaux et Télécommunications 1650 Blvd. Lionel Boulet C. P. 1020, Varennes Qc, Canada J3X 1S2 _Tél:_ (450) 929 8220 _Fax:_ (450) 929 8102 _Courriel:_ [EMAIL PROTECTED]
Re: GSAS information (anisotropic microstrain)
Andreas, What you say is good to know. Nonetheless, the type 4 profile model has built-in constraints according to the cell class -- so it is easy to use and refines with far greater stablility that the Lxx terms. My advice to non-experts is still the following: If you suspect that you have some reflection classes having peak widths wider than others, try out the type 4 model -- refining the Sxx terms and then eta. If the fit improves significantly, you likely have anistotropic peak broadening. If not, you don't go back to using the type 3 model and ignore the L tensor. The Stephens model is correct only for strain broadening -- but my experience is that it does a pretty good job fitting other types of anisotropic broadening, for example anisotropic crystallite size broadening. In the cases where pretty good is not good enough, then it would make sense to check out the Lxx terms -- but only after trying the Type 4 model to confirm that the observed broading indeed does vary by reflection class. Brian Andreas Leineweber wrote: Dear Brian, recently it was pointed out (J. Appl. Cryst. 37 (2004) 123-135) that the approach proposed by Von Dreele can have indeed - under certain circumstances and restrictions to the parameters - a physical meaning, e.g. concentration fluctuations can show up like this, and the type of anisotropy constitutes a special case of the Stephens model. Best regards Andreas Leineweber Brian H. Toby wrote: My advice on this question is that one should not use this approach. The Stephens formalism, coded in profile type 4, is better founded by theory. See the GSAS manual and reference to Peter Stephen's J. Appl. Cryst paper from a few years back. Brian Christophe Chabanier wrote: Hello everybody, i have a question about the GSAS software. Indeed, i would like to know what are exactly the L11, L22, L33L23 parameters. I saw that these parameters represent the anisotropic microstrain in material. Moreover, there is an empirical expression which uses these parameters as following : Gamma(L) = L11*h^2 + L22*k^2 + L33*l^2 + 2*L12*hk + 2*L13*hl + 2*L23*kl I would like to know and understand the physical representation of these parameters and this expression. Thanks in advance Christophe Chabanier INRS-Énergie, Matériaux et Télécommunications 1650 Blvd. Lionel Boulet C. P. 1020, Varennes Qc, Canada J3X 1S2 _Tél:_ (450) 929 8220 _Fax:_ (450) 929 8102 _Courriel:_ [EMAIL PROTECTED]
Note to software designers
Maxim V. Lobanov wrote: U, V, and W tend to be highly correlated, with a result that various combinations of quite different values can lead to essentially the same variance, sigma^2.These three parameters, therefore, do not converge in a stable manner when refined simultaneously (Prince, 1993). As Ted Prince also pointed out, if the Cagliotti equation is given an origin shift, e.g. U tan2(theta-theta0) + V tan(theta-theta0) + W where theta0 is fixed at 1/2 the monochromator off-angle, the correlation in these parameters is greatly reduced. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: RIET:STX:Latest IUCr Commission on Powder Diffraction Newsletteron-line
Paolo, I am not sure who I should tell, but the US page (http://www.us.iucr.org/iucr-top/comm/cpd/Newsletters/) is very far out of date w/r to the main site (it lists issue #22 as the most recent). Brian Lachlan Cranswick wrote: Sent on behalf of Paolo Scardi: The IUCr Commission on Powder Diffraction issues a free hardcopy newsletter that is available to anyone who contacts the CPD chairman to get added to the distribution list: prof. Paolo Scardi (E-mail: [EMAIL PROTECTED] ) As explained below, a PDF version is also available: No. 25 of the CPD Newsletter is devoted to Structure Solution from Powder Diffractometery (SDPD) with Bill David of ISIS - CLRC Rutherford Lab, UK as the editor: In this issue there are articles by I Madsen, D Balzar, A Le Bail, L M D Cranswick, L B McCusker, Ch Baerlocher, T Wessels, P Sieger, R. Dinnebier, K Shankland, W I F David, P W Stephens, S Pagola, D S Bohle, A D Kosar, A N Fitch, G B M Vaughan, A J Mora, R B von Dreele, L Smrcok, M Durik, K M D Harris, R L Johnson, E Tedesco, G W Warner, N Shankland, A Kennedy, C S Frampton, A Florence, A Altomare, C Giacovazzo, A G G Moliterni, R Rizzi, The PDF of the newsletter can be viewed (as well as back issues) via the IUCr website or any of its mirrors: http://www.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.se.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.ch.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.us.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.au.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.za.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.il.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.fr.iucr.org/iucr-top/comm/cpd/Newsletters/ http://www.ru.iucr.org/iucr-top/comm/cpd/Newsletters/ As a bonus, Outcomes of the International Union of Crystallography Commission on Powder Diffraction Round Robin on Quantitative Phase Analysis samples 1a to 1h: Ian Madsen, Nicola Scarlett, Lachlan Cranswick and Thuang, Lwin can also be downloaded via the link Annex to the newsletter (1.8MB) The next issue of the CPD Newsletter will be edited by Robert Dinnebier to appear in autumn of 2001. Robert will greatly appreciate contributions from readers on matters of interest to the powder diffraction community, e.g. meeting reports, future meetings, developments in instruments, techniques and news of general interest. Please contact him for sending articles and suggestions. Software developments can be addressed directly to Lachlan Cranswick; or to the Editor of Newsletter No 26: Dr R. E. Dinnebier (Robert) Max-Planck-Institut fur Festkorperforschung Heisenbergstrasse 1 D-70569 Stuttgart Germany E-mail: [EMAIL PROTECTED] --+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+ --+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+--+ Lachlan. --- Lachlan M. D. Cranswick Collaborative Computational Project No 14 (CCP14) for Single Crystal and Powder Diffraction Birkbeck University of London and Daresbury Laboratory Postal Address: CCP14 - School of Crystallography, Birkbeck College, Malet Street, Bloomsbury, WC1E 7HX, London, UK Tel: (+44) 020 7631 6849 Fax: (+44) 020 7631 6803 E-mail: [EMAIL PROTECTED] WWW: http://www.ccp14.ac.uk -- Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
latest GSAS version: for SGI and Linux
Hi folks, I have recently completed compiling the latest version of GSAS (dated June 11, 2001) for the Silicon Graphics and then verifying it with the test suite. This will be the first time in more than 3 years that the SGI version has been updated and it is identical (one hopes) with latest the Linux and Windows versions. There is a fair chance I have not gotten things right, (for example by not included all the appropriate files in the distribution), so I would like to work with a few volunteers on the install of this version to see how it goes before giving it over to Bob to put up at Los Alamos. If you are interested, please respond to me at [EMAIL PROTECTED] (please don't reply to this e-mail and bother the entire Rietveld list). At Bob's suggestion, I have made an RPM file to install the same versions of GSAS and EXPGUI in one fell swoop (swell foop?) for Linux. I have done some testing with Redhat 6.2, 7.0 and 7.1, but I would like some feedback on how it goes with users, particularly with non-Redhat versions of Linux (but don't bother with anything much older than RH 6.2). Again, contact me and I'll tell you what to do. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: new GSAS (EXPGUI)
Anthony Manerbino wrote: Is the program expgui used instead of the routine expedt for entering structural information and bring experimental patterns into GSAS? In a word, yes. EXPGUI does only a fraction of what EXPEDT does, but I would like to think it is pretty useful. See http://www.ncnr.nist.gov/xtal/software/expgui/expgui_intro.html for more info. Brian P.S. The current version should work fine with the latest GSAS release for Windows, but I have not yet gotten my act together for the "beta" Linux release. ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Neutron diffraction with boron
Armel Le Bail wrote: Have new neutron powder patterns been done on the magnesium diboride superconductor yet (or derivatives, if any), or B absorption will be a too big problem ? Yes, neutron absorption by boron is a potential problem, however use of 11B in place of natural abundance boron eliminates the absorption. This isotope is available fairly readily. And yes, the measurements have been done. People contemplating neutron experiments may want to estimate absorption using http://www.ncnr.nist.gov/xtal/neutron.html Brian News Flash: The unscheduled mantainence for the NIST reactor has been postponed until our scheduled upgrade in August. We plan to resume operations in about 2 weeks. Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: GSAS profile #4 FWHM
WIDPLT will not properly handle the type 4 profile function. Marc's suggestion is good, but it works only for a limited set of reflections, but not the general case. Furthermore, LY is for Cauchy (Lorentz) broadening, this is true with the Sxx terms only when eta=1. With eta=0 this broadening is Gaussian. A better solution would be to be able to plot the width along a preset vector (100, 111, 531, whatever) but I have no plans to do this anytime soon. If anyone is so inclined, they could do this themselves (the WIDPLT code is in the gsas/expgui directory). I seem to recall that the one-phase option in REFLIST prints a list of reflections and their FWHM. This may be a better way to solve your problem. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal Xiang Ouyang wrote: Dear Marc Hostettler, Thank you for help. I should calculate FWHMxxx in the widplt (U,V,W,P,LX,LY) with Sxxx replace the LY. I will give it a try. Sean X. Ouyang Marc Hostettler wrote: On Thu, 22 Mar 2001, Xiang Ouyang wrote: Hello Colleagues, In GSAS CW profile #4, there are parameter U, V, W, P and LX, but no LY. how should the FWHM be calculated? I used Widplt (in Brian Toby's EXPGUI) to plot the FWHM of a pattern fit with profile #4 and the FWHM descent with 2 theta (U = 0, V = -2.3, W = 3.75, P = 0, LX = 0.8, eta = .6). Any help? Peak profile type no. 4 in GSAS allow to modelize anisotropic peak broadening (see Stephens J.Appl.Cryst. 1999), therefore LY is parametrized for each set of reflections H00, 0K0, HK0... The corresponding parameters being S400, S040, S220... Best, Marc Hostettler Lausanne
EXPGUI update
A new version of EXPGUI (a graphical user interface for GSAS) has been placed on the NIST and CCP14 websites. (see http://www.ncnr.nist.gov/xtal/software/expgui/expgui_intro.html) This version fixes a bug with setting the Fobs extraction flag and places all of the recent upgrades from the alpha version into the "standard" version. Users of the most recent versions of GSAS (DOS/Windows/Linux but not yet SGI) should update if they want to turn on extraction of Fobs or do a LeBail extraction from EXPGUI. I am also interested in getting suggestions for new features to be added to EXPGUI. Please write to me directly. Brian ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
EXPGUI bug (was Win-GSAS question/problem)
[EMAIL PROTECTED] wrote: - if we start to load the *.gsa file (not only ours, but also the one coming with the program) we get the following output ... EXPTOOL (P,H,A) Enter raw histogram input file name Enter ... (?,A,B,C,D,E,F,I,L,M,P,S,T,W,X) run-time error M6103: MATH - floating-point error: divide by zero Sorry, this one is my fault. This error is due to a bug in EXPGUI that allowed one to add a histogram before defining a phase. This was fixed in the "alpha" version of EXPGUI a few months ago, but has not yet made it into the "stable" version. BTW, I just sent out to the EXPGUI mailing list an e-mail message explaining recent changes in the latest "alpha" version that should improve a number of problems in windows. If you use EXPGUI and are not on this list, send a message to [EMAIL PROTECTED] and I will add you so that you are notified of EXPGUI updates (Note: don't reply to this message! Netscape users can click here mailto:[EMAIL PROTECTED]?subject=EXPGUI+Mailing+List to reply). If you use EXPGUI and don't want to be bothered with e-mail, I would still like to have your name -- but tell me not to put you on the list. After I get some feedback on the impact of these changes, the "stable" EXPGUI version will be updated. Happy Hannuka, Christmas, Ramadan, Diwali, Kwanzaa or whatever, Brian ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
more ranting on databases
The question "who really possess the copyright" of such data mainly produced at academic research institutions has no clear answer. Not so. I am no expert on copyright laws, but I do believe one can obtain copyright protection on a collection of information, even if the contents are in the public domain, provided that the collection itself is new. Further, one can copyright the way information is formatted. Finally, corrections, reference numbers or other cataloging information added by the information compiler is also subject to copyright protection. I am pretty sure of this for the U.S.A. and suspect this is true in most of the world. What does this mean? As a U.S. government employee, my research is not subject to copyright -- anyone in the world can use my software, structures,... in any way they choose and I am glad to contribute it. (Congress specifically exempted reference data from this rule, BTW). On the other hand, if one goes to the library makes and distributes 10,000 photocopies of a table of coordinates from one of my papers, that is a violation of the journal's copyright. (Sending one copy to a friend probably does not violate the copyright, since there is an exemption for "scholarly purposes".) What if you retype/reformat the coordinates and then make 10,000 copies? In this case I'm not sure, but since the crystallographic data are not protected, I suspect this is indeed legal. What about coordinates from, say, Armel's papers? That depends on the copyright agreement Armel made with the journal. He may have given ownership to the journal. Depending on that agreement, perhaps even Armel will be limited in what he can do with "his own" data. So, contrary to the assertions made on this mailing list, when you republish crystallographic data, using a database's format and/or include information generated by the database compilers, you are probably violating their copyright. If you reformat the information and restrict yourself to the data that appeared in the original article, then things are less clear and probably depend on many factors. All the legal B.S. aside. I personally would like to see crystallographic databases made widely and cheaply available. Given that no government seems to want to pay to give them away, they probably will never be free. Volunteer efforts, like Armel's powder data repository (http://sdpd.univ-lemans.fr/powbase/index.html) could change this -- if lots of folks contribute -- now that gigabytes are cheap and web access is nearly universal. Such efforts also have the potential to keep database pricing in line by providing an alternative. I am no great friend of database "vendors." I have gotten in trouble for publicly criticizing the representative of a database organization that charges exorbitant prices to U.S. companies who want occasional access to their data compilations. But, this is not the case with the ICSD: * they offer a very good academic discount; * they allow pay-as-you-go searches via STN for the person who does not want to pay for 100 000 entries when you need, say, 10 data sets in one year; * even their commercial price seems pretty reasonable (to me) compared to some of the other databases. Microsoft may or may not set prices based on the the number of people who buy their products, but the ICSD academic discount would not exist, if not for all the folks willing to pay it. I will not defend Bill -- but please don't rip off the folks who are doing all the right things. Brian (The above represent my own opinions and will probably get me in even more trouble).
Re: Natrite - Na2 CO3
Uwe Kolitsch wrote: (by the way, the ICSD costs only 500 US dollars per year). A company such as USG would not be able to lease the ICSD at the $500 academic price. I no longer remember the for-profit price, but it is significantly more. However, these prices cover the cost of tabulating the data -- and would likely come down if more people subscribed rather than pirated the contents. It is a shame that a company that describes themselves as "... the world's largest producer of gypsum wallboard, joint compound and a vast array of related construction products. As North America's number one building materials manufacturer and distributor, we are also number one in the North American wallboard and joint treatment markets and number two in the ceilings market. "With 249 worldwide locations and more than 14,000 employees, USG is dedicated to providing innovative building solutions that set new standards for productivity and efficiency, helping contractors and architects deliver better quality and innovative designs, and maintaining strong ties with our customers while expanding our global distribution reach." has to resort to requesting structural data via this mailing list. Brian Toby (This opinion is my own and not that of my employer)
Re: Thermal Parameters and Occupancies
Caroline, This is a very thorny issue. In general, displacement [nee thermal] parameters correlate highly with occupancy. With x-ray data, while refinement tricks may allow both to be refined, there is not typically enough data to allow both to be determined. With neutrons, the problem is not as severe but is still present. With neutrons one can sometimes refine both Uiso and the occupancy, but even then sometimes one needs to fix or group the displacement parameters. It helps to have a feel for what reasonable Uiso values are, but this is a function of the material type, temperature and the atomic mass. My recommendation to perform a sensitivity analysis at the end of the refinement to see if the occupancy values are significant. I typically take the final Uiso and fix it at the final value divided by 2 and multiplied by two and refine the occupancy each way. If, with both extreme Uiso values, I see occupancy values similar to my refined value, then I am willing to accept that the occupancy value is likely to be "real" rather than an artifact of the fitting procedure. Brian "C.A.Kirk" wrote: Dear All, I have a question regarding the correlation of thermal parameters and occupancies. If anyone could give some tips on achieving a satisfactory conclusion/minimum during a refinement, it would be greatly appreciated. At the moment I refine the atomic positions then the Us until a minimum is reached. If a U is particularly high, for instance, then I check the occupancy of this site; sometimes partially occupied sites are expected in the phases we study. However, as the U is fixed at the refined value then this willeffect the occupancy. As I understand it the refined U is for the occupancy fixed during the refinement. Sometimes a change in the occupancy is observed on refining. I then will alternate between refining the occupancy and U until a minimum is reached. Is a better strategy to fix the U at a value for the same atom type in the phase and look at the effect this has on the occupancy? Explainations, suggestions, tips, further reading welcome! Caroline Caroline Kirk Solid State Research Group Department of Engineering Materials University of Sheffield Sir Robert Hadfield Building Mappin Street Sheffield S1 3JD Telephone: 0114 222 6013 E-mail: [EMAIL PROTECTED] -- ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: SRMs 640c 660a
Luca Lutterotti wrote: Sorry for the question, but I personally and philosophically don't think we can measure absolute values.. Hmmm, In that case, I guess you should persuade the USA to change the name of my employer. I disagree. There are such things as fundamental properties and they can be measured. It takes careful work to plan an experiment so that measurements are referred to primary constants, for example in this case the fundamental length reference. I am glad I don't have to do this sort of work myself, but have great respect for the folks that do. It should be noted though that the certified lattice constant for a standard reference material is something measured on a real specimen (that must be available in ~100 kg quantities) under the sorts of conditions likely to exist in the lab setting where the SRM will be used. This is different from a fundamental constant, such as the lattice parameter for one single crystal specimen of ultrapure Si, under a highly controlled environment. Since the materials and conditions differ, one would expect the lattice constants to differ too. Likewise, since the SRM 640, 640a, 640b, materials physically differ, both with respect to impurities and with respect to processing, one would expect their lattice constants to differ, too. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: mixing parameter
Holger, I am not sure how to answer your question, but perhaps this will help. A pseudo-Voigt is the sum of a Lorentz function and a Gaussian function and simulates a Voigt, which is their convolution. There are two ways to parameterize a pseudo-Voigt. One is to have the same peak widths for both the Lorentz and Gaussian functions and then use a mixing parameter (eta) where 0 is pure Gaussian, 1 is pure Lorenzian and 0eta1 is a mixture. There is a different approach, where the Lorentz and Gaussian functions each have their own parameterization. (I think that Bill David wrote something about this a while back). GSAS uses this latter approach. For CW profiles 2 3, the primary terms are Gaussian: GU, GV GW; Lorentzian: LX LY. Do read the GSAS manual, there are many more terms that have specific uses. In profile type 4 (not in the manual), there is an appearance of our friend eta. In this case it is the mixing parameter for the treatment of anisotropic strain broadening. See Peter Stephens J. Appl. Cryst. paper for info on that. Brian Holger Kohlmann wrote: Hi, coming from FullProf and trying a first refinement with GSAS I am a bit confused about profile functions for CW data. How can I refine the mixing paramter eta in a pseudo-Voigt function with GSAS? - Holger Kohlmann -- Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: Powplot problems with NT
Brian Mitchell wrote: I have recently installed Windows NT on my laptop and find that the GSAS graphics plot takes an excessive amount of time to appear. I did not have this problem with Win 98. Any help/advice appreciated. My suggestion is to upgrade to Linux. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
Re: Lp correction in GSAS
Marek, There are three polarization functions listed in the manual, but only 2 when I try to select the function in EXPEDT. I seem to remember that the 1st two functions are equivalent, other than scaling, but I am not going to work this mystery today. As I recall, with IPOLA=0 (RBVD Lp correction) POLA sets the relative amount of in-plane vs out-of-plane polarization coming off the incident monochromator. Thus for you, POLA should be slightly less than 1.0 (synchrotrons tend to be highly polarized, but the actual amount depends on many factors). I have used 0.95 to 0.99 for my work at X7A. The bad (or good) issue here is that the P part of the LP correction is virtually indistinguishable from the Debye-Waller 2theta curve, which means if you refine it, the displacement parameters (aka "thermal" factors) couple to POLA and you can refine to an unrealistic value, like 1. If you fix POLA to a wrong value, your displacement parameters shift to compensate. For that matter, absorption corrections have ~ the same form, too, particularly since you have data over such a small Q range, so that will also interact with POLA and displacement parameters. Pick a value of POLA and fix it. Someone at the beamline you used must have a rough idea of the right value. If you are really adventurous, pick a few values and compare the results of the different refinements. That will give you a feeling for the impact of POLA on your results. Brian ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal Marek Schmidt wrote: Dear All, I have two questions concerning the polarization factor in GSAS. I am analyzing synchrotron x-ray diffraction patterns and to work out the diffractometer constants I refined a silicon pattern. My questions are: 1.What is the formula for the RBVD Lp correction? Is it the third formula on page 125 of the manual? 2. The pattern was refined using the RBVD correction. The refined polarization fraction POLA reaches a value of 1.14 (the initial value was set to 0.95) is it possible? The experiment was carried out in Debye-Scherrer geometry with an incident beam monochromator and the patterns were collected using imaging plates. The camera radius is 573mm, the sample was placed in 0.3mm glass capillary. The refinement includes absorption correction and corrections to the silicon scattering factor (f' and f"). Wavelength= 1.796A, the angular range is 5-150deg. Best regards M. Schmidt == Marek W. Schmidt Department of Applied Mathematics Research School of Physical Sciences and Engineering Australian National University Canberra ACT 0200, AUSTRALIA email: [EMAIL PROTECTED] facsimile: 61-2-6249 0732 telephone: 61-2-6249 0381 ==
IUCr policy statement on STAR/CIF
dictionary to define data items in terms of "attributes". Dictionaries currently approved by the IUCr, and the DDL versions used to construct these dictionaries, are listed at http://www.iucr.org/iucr-top/cif/[...URL to be completed...] - - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT - DRAFT -- ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562 http://www.ncnr.nist.gov/xtal
[Fwd: Announcing a new discussion list for developers of CIF software]
The discussion list described below will be of interest to anyone wishing to develop software that reads or writes CIF files. (I sure hope there are at least a few people in the powder community who fit that description.) Brian Announcing a new discussion list for developers of CIF software. The Crystallographic Information File (CIF) sponsored by the IUCr is a standard for information interchange in crystallography. First published in 1991 to describe single-crystal experiments and data for small-molecule structures, CIF now covers macromolecular structure determinations and powder diffraction studies, and extensions are under development for image data, modulated aperiodic structures and other techniques and disciplines within crystallography. Although each CIF application uses the same basic file syntax, content is determined by external files (known as data dictionaries) that specify the relevant data model and carry information about data typing, validity and interrelationships. While customised applications can be written to utilise specific sets of subsets of CIF data, the most powerful applications are dictionary-driven, so that they can use or be easily modified to use new sets of data items as they are released. Authors of software capable of handling CIFs are invited to subscribe to a new discussion list for the sharing of experiences, information and code. The list is open to anyone with an interest in developing software that is compliant with the published standards for reading and writing CIF data, and is also relevant to developers of software for the more general STAR File structure that defines the syntax of CIFs. Authors of publicly distributable software are especially welcome, but authors working in a commercial environment will also benefit from membership. The one strict condition imposed by the IUCr on CIF-compliant software is that it should indeed comply with the standard; it is hoped that the existence of a list such as this will halp developers to work within the standard, and to develop robust cross-platform libraries and tools for general use in the community. Mailings to the list should be sent to the address [EMAIL PROTECTED] To subscribe, send an email message to the address [EMAIL PROTECTED] that contains a line of the form subscribe [EMAIL PROTECTED] your-name Further details may be found on the web page http://www.iucr.org/iucr-top/lists/ Initially the list will be moderated (though the list manager reserves the right to moderate responses if there is an unacceptable level of junk mail); an archive of discussions will be accessible via the web at the URL indicated above. A supporting web page for developers will be maintained by the IUCr COMCIFS team at http://www.iucr.org/iucr-top/cif/developers.html, which will include a Frequently-Asked Questions (FAQ) page. Please forward this invitation to colleagues who may also be interested in this list. Brian McMahon, IUCr, Chester, UK Coordinating Secretary, COMCIFS [EMAIL PROTECTED]
Re: Kalpha2
Dr.Joerg Bergmann wrote: Indeed, such simple crystal measuring is unable to detect tube tails. Tube tails are out of the Bragg-Brentano focusing conditions. That means their diffraction vector is not orthogonal to the specimens surface (to the lattice planes of the single crystal). So, single crystals do not reflect tube tails. I have been trying to follow this discussion with little success. Perhaps I am missing something, but if you can't see these tube tails in a measurement with a single crystal (where signal to noise is optimal), why would you see the effect with a powder, which is a collection of single crystals? What is different about the physics of the powder experiment that allows this tube tails phenomenon to be observed? The only difference I see is Bragg-Brentano focusing, which is effectively disabled by the narrow Darwin width of the single crystal. Could someone please elaborate? Thanks, Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: Asymmetry
One other reference worth noting is Ted Prince's paper in J. Appl. Cryst [p508-511 (1983). "THE EFFECT OF FINITE DETECTOR SLIT HEIGHT ON PEAK POSITIONS AND SHAPES IN POWDER DIFFRACTION"]. Ted has a single-parameter asymmetry model that is computationally simpler than the Finger-Cox-Jephcoat (though perhaps not as general). Also, in the interest of fairness, the first implementation of the van Laar Yelon approach is a paper by Mike Eddy, Tony Cheetham Bill David: Zeolites, p449 (1986). Brian Bruce A. Weir wrote: Does anyone know of a good reference which discusses peak asymmetry in low angle X-ray powder diffraction data? ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: New version of PC-GSAS
Bob, Hurray! Are you including tcldump exptool in your distributions? If not, could you at least compile them as you do each platform? Let me know anything I can do to help. Brian
CMPR for Windows and UNIX
I have updated CMPR. Documentation can be found at http://www.ncnr.nist.gov/programs/crystallography/software/cmpr/ (and within a day or so, the ccp14 mirrors, http://www.ccp14.ac.uk/mirror/) For people who have not used CMPR, it reads powder data in a variety of formats, plots data in multiple formats, does peak fitting (optionally with the Finger/Cox/Jephcoat asymmetry correction) does manual powder indexing and shows extinction conditions. It runs under Windows and UNIX with the same graphical user interface and the same features. It is written in Tcl/Tk so that anyone can add new features (no compiler needed). Please send mail to [EMAIL PROTECTED] (don't reply to this message!) if you use CMPR so that I can add your name to the mailing list for notice of future updates. I will not announce them in [EMAIL PROTECTED] Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: gsas in dos UNIX
Roger Mason wrote: Does anyone know if it is possible to use the same *.EXP file on dos UNIX (Linux) machines? If so, what changes must be made to the file? The file contents are exactly the same for the .EXP as well as the data and instrument parameter files, but in DOS the records must be exactly 82 characters per line, including the CR-LF terminator. In UNIX the files should be exactly 80 characters per line with no terminators. To xfer files from UNIX to DOS you need to add a terminator or else when the files get into DOS, you have one huge record that is very hard to work with. This can be done in UNIX with the GSAS CONVDTOS program. (DTOS = Direct-access to Sequential). One the files are in DOS, you then format them using the CONVERT program in GSAS that adds the CR-LF terminator. To go from DOS format to UNIX, run CONVSTOD. The version of CONVSTOD/CONVDTOS that is in the current release of GSAS is full of "features." For example, it will ruin files that are converted twice. (My fault not Bob.) A newer version can be found at ftp://ftp.ncnr.nist.gov/pub/cryst/gsas/cconvstod.c with compiled versions at ftp://ftp.ncnr.nist.gov/pub/cryst/gsas/exe_XXX/convutil.tar.gz (XXX=SGI and linux). [Link the executable to .../gsas/exe/convstod and .../gsas/exe/convdtos and run from the menus or from the command line as .../gsas/exe/convstod input output The sequential files produced by this version of convdtos are in the DOS format. It does not screw up the file, if you convert a file that is already in the correct format. Brian ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: Data Format
[EMAIL PROTECTED] wrote: I would just like to draw your attention to the NeXus project, which has the (ambitious) purpose of developing a unified data format for x-rays and neutrons. http://www.neutron.anl.gov/NEXUS/ http://lns00.psi.ch/NeXus/ The NeXus format is an excellent way to deal in binary with the large amounts of data generated by many energy-dispersive and PSD instruments. CIF stinks for this and my impressions are that imgCIF is a Band-Aid that is far less versatile than NeXus. NeXus is also designed for other types of scattering experiments than diffraction. The unanswered question that faces the powder-diffraction crystallographic community is, if crystallographers standardize on CIF for communication of structural results (pretty much a fact already) and major neutron and x-ray sources standardize on NeXus (pretty likely), how does the gap get bridged? Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: RIET: Re: [sdpd] Re: Use of CIF as advocated by Lachlan
Robin Shirley ([EMAIL PROTECTED]) writes: However, I have to say that I'd feel happier about supporting CIF as a common file format if (a) it were considerably simpler to read and (b) the CIF committee were more responsive to practical powder-related issues. I do owe Robin an apology for my inaction. I have still not completed all the tasks I have promised with respect to pdCIF v1.0 and so I have not started work on v1.1, which will incorporate some of the additions suggested by Robin and others. CIF is something that I work on at home, not as part of my employment and time for it is scarce. A volunteer to take over for me would be very welcome. L. Cranswick wrote: PS: With respect to Robin's comments on trying to get additions to PowderCIF for Powder Indexing,;what is the present mechanism for getting things implemented into the Powder CIF area? As of right now, the procedure is to read through the pdCIF dictionary to determine what it is you want to store that is not present and then define the term to be added. You then write to me with a case for why the terms are necessary and then let your e-mail age in CIF inbox for a while. A IUCr committee (pdDMG) will eventually evalute these suggestions. I hope to be ready to start this soon. I would like to note that while there is a lot of information that can be stored in a powder CIF, software that reads CIFs needs only to deal with the relevant fields for the task at hand and can ignore the rest. While CIF has provisions for including structural information, peak and reflection tables,... life does not need to be so complex. For storage of raw lab data, one can write a very simple CIF file that looks like this: data_myCIF _pd_meas_2theta_range_min 5.0 _pd_meas_2theta_range_max 65.0 _pd_meas_2theta_range_step 0.02 loop_ _pd_meas_counts_total 10 16 23 18 ... That's it! Not so complex. Of course it would be a good idea to use the appropriate CIF terms to describe if the data are x-ray or neutron, specify wavelengths used, if a theta-compensating slit was used,... As many people keep rediscovering, ambiguous data can be very hard to use. (Does NEXUS just handle data - or can it include structure information?) There is no reason that NeXus could not include any kind of information, but no provisions exist as far as I know. It is really being implemented as a raw data format. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: Bond length and angle ESDs
Is there a program which can take as input the atomic positions and lattice parameters and the associated errors and give as an output an estimation of the bond lengths, angles and associated errors? I think that doing this would give an overestimation of the errors (for example it neglects any correlation in atomic positions) even if such a program exists. This may be a pedantic point, but standard uncertainties (aka esd's) really should be estimated using the covariance matrix. If you estimate uncertainties without using the correlation information in the matrix, your results can be significantly higher or lower (or unchanged) depending from the best estimates, depending on the sign and magnitude of the correlation coefficients. It has been a couple of decades now, but I seem to recall modifying ORFEE for exactly this purpose -- reading atomic parameters and the covariance matrix from a refinement program to get distances and angles with S.U. I suspect Larry Finger's program BONDAN and many others could be adapted as well. Brian
Re: Help: find calculated peak intensities/areas in GSAS
Turn on intensity extraction (in least squares options menu) Tao wrote: Dear All, I have problem in finding calculated peak intensities/areas in GSAS. Someone told me to use "reflist" command and look in its output list, but the result doesn't make sense to me: the columns under "Fosq" and "FoTsq" are all zero, and those of Fcsq and FcTsq a The first couple of lines from reflist output is copied below: Iref H K L Mul Icod D-spaceFosq Fcsq FoTsq FcTsq 1 0 0 3 2 1021 4.68645 0.000E+00 2.574E+05 0.000E+00 6.972E+03 2 0 0 3 2 1121 4.68645 0.000E+00 2.574E+05 0.000E+00 6.972E+03 3 1 0 1 6 1021 2.40416 0.000E+00 7.497E+04 0.000E+00 3.426E+03 Could anybody kindly help me out here? Many thanks in advance, Tao 5/11/99 -- ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Combined neutron/x-ray refinements
I also use combined CW neutron and synchrotron refinements. A simple minded justification goes as follows. Most of the problems I work on are badly underdetermined -- at least by the crystallographic rule-of-ten (10 crystallographic observations for each structural variable). By changing scattering lengths, I get a second set of observations which gives me more observables. Thus, I agree strongly with all of Dr. Jaap Vente's points: 1) in general the refinement is more stable. 2) their is the possibility to study much more complicated structures than with only one of the techniques. 3) because you now have two really different sets of data your structural model is more reliable. 4) you can study compounds which contain elements that are difficult to locate precisely with one technique, think of vanadium oxides or manganese/iron oxides. Andrew Wills is correct that X-rays see the electronic distribution and neutrons see nuclei positions, but electrons distributions are pretty close to spherical (our form factors assume this) for high-Z elements and are usually well centered around the nucleus. One can make a good argument that displacement parameters (aka temperature factors) can be completely different for x-rays vs neutrons, but experimentally this is seldom true. In any case, for all but the simplest systems, with powder work we don't have the precision to tell. Besides, x-ray displacement parameters are pretty meaningless anyway :-). I do not know of any codes other than GSAS that do combined x-ray/neutron fits, but in GSAS all the experimental effects (orientation, absorption, etc) are segregated by dataset so one only needs to apply these corrections to the x-ray data. (Neutron data seldom have either problem). In any case, if you can't model them well, you can't use the data. The "weighting" problem is overstated. The data are weighted by how well you know them. Usually the x-rays do contribute more to the Chi2 than the neutron, but the algorithm will minimize the deviations in both appropriately. One could downweight the x-ray data artificially, since you will probably have worse precision on the more structurally accurate neutron data, but this will screw up the Chi2 value. The biggest problem for combined refinements is that you need to have exactly the same sample and the same conditions for both the x-ray and neutron work. Since single crystals are frequently grown under different conditions than bulk samples, the utility of combined x-ray single crystal - powder neutron refinements is limited. Alas, it is fairly common that someone makes a material, measures the x-ray diffraction and then scales up the synthesis for neutrons, but ends up with something different. Attempts to simultaneously fit one model to x-ray data from the first batch and neutron data from the second batch are a waste. Other issues can also arise. We recently had a case where a material seemed nearly pure by x-rays, but the neutron work showed that the centers of the large particles were still composed of unreacted starting material. The x-rays did not penetrate far enough to see the purity was only ~70%. It would probably be a good idea to check that the model obtained from the combined refinement agrees well with (possibly constrained) models using the individual datasets. Perhaps we could entice John Parise to write a message about how to do this. Finally, I should mention in response to Armel that at least here at NIST, most requests for time are scheduled within 2-8 weeks of when we get them (see http://www.ncnr.nist.gov/~toby/bt1.html). ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: Comments on Importance of matching software with hardware
Plotting in Q sounds good to me.
Re: looking for ICSD data...
I can understand the annoyance that is raised w/r to the industrial cost for ICSD. My pet peeve (as a former industrial chemist) was the cost for the Cambridge Crystal Structure Database, where academic users could get it for some small amount ($500 for a site license as I recall) and industrial users pay a huge amount (~$30,000/year ?). My department could not afford it, so we used the library and typed in coordinates. The argument for this pricing is that industry (particularly for CSD, the pharmochem community) uses this data to make money, while academic users are the producers of the data in the database. There is clearly a problem with this one-price-fits-all scheme for industry, but I wonder if the people complaining will change their price for their products/services for a customer who can't afford more, if they feel that it will impair their ability to collect full price from the customers that can afford the fee. In the case of ICSD, the US industrial cost is ~$8000 for the 1st year and then ~$4000/year for subsequent years. This is for a site license. There may be a discount for site licenses for academic and non-profits, but I know we at NIST pay close to full price. True, there is a low price for *individual* academic users -- for the DOS version only, and if you want 10 professors/students to have copies, pay 10 times. So this is not a 90% discount. Unlike all of the other crystallographic databases, you can pay to search ICSD database without buying it; ICSD is available as part of the STN service (www.cas.org). I wish that that were true of the rest. So at least in this case, they are not "locking up" the data and forcing one to buy it just to get occasional access. As for the copyright issue. One can copyright a collection of information even if the all the components of the collection are public domain. The collection, for example a volume of poetry, becomes more than just the sum of the contents -- the selection of what items to include and their order matter. As such, the ICSD is a copyright-protected collection. You may be able to access any of the data inside the ICSD in a library, but that does not allow you to make copies of large sections of the database and give them away. I would not think any commercial scientist would want the intellectual property they create to be pirated either. Personally, I would like to see the databases become much cheaper for both industrial and academic users, but for that to happen academic use needs to become more mainstream and perhaps the argument needs to be made with the database suppliers (not me) that their commercial pricing needs to be restructured. So the next time someone writes a message "can anyone tell me about..." I would like the reply to be "There are XXX entries in the ICSD database, you should get a copy or search it on STN. Failing that, here is a literature reference to get you started ...". I can see the occasional exception for the scientist in a less affluent country, but ironically they seem to be able to afford ICSD. In my experience, the vast majority of the requests seem to come from students at large US universities. Brian Karsten Winter [EMAIL PROTECTED] wrote: This is where the crunch lies. I am, for example, a private NON-academic crystallographer... and there is no allowance for people like me. We can only buy the "Industry-version" for 10,000 DM (~5,800 US$). And frankly: I do not have the pocket money to buy it... people in academic institutions seem to forget that there is a world outside their protected space. [EMAIL PROTECTED] wrote: Can anybody explain to me the factor of 10 difference in price for ICSD data between academic and industrial users. Is there a rational explanation or a formula which makes an industrial dollar buy only 10cents when shopping at ICSD? I know of discounts given to academic users for commercial software which is of the order of 30 to 50%. But to give merchandise away at 90% discount to one group of people and charge another group the full price (whatever it may be), I have a problem with that. This, by the way, is the reason why there are so many requests these days - the market reacts to such humbug. L. Keller CAMET Research, Inc. Goleta, CA
Re: structure factors calculation
Hi Pat, Not everything requires a computer, even though I have a reputation for liking to use them. Going back to Stout Jenson, one finds F(hkl) = SUM f(i) EXP[2 pi i * (hx + ky + lz)] [since you are ignoring displacement (nee thermal) factors] For the FCC case, you have 4 atoms at (0 0 0), (1/2 1/2 0), (0 1/2 1/2), (1/2 0 1/2) So if you pick one of your reflections, say the 111, then F(111) = 4 f(Ni) For lambda= 1.5418, 2theta = 44.53 (I cheated a bit here and used a computer to get 2theta rather than looking up a0 for Ni in a book) and sin(theta)/lambda = 0.246 ~= 0.25, so f(Ni) ~= 20.39, using Volume C. so F(111) ~= 81.56, which is pretty close to the powdercell value and would probably be closer if I interpolated to get f at sin(theta)/lambda=0.246 rather than sin(theta)/lambda=0.25 Why then does lazy-pulverix give 77.4? Well, looking at the printout, one sees that the default for B is 1.0, so adding the "thermal" term, exp[-B * sin2(theta)/lambda2] = 0.94, I get F(111) ~= 76.78, which is pretty close to the lazy-pulverix value. End of mystery, I hope. I will leave computing F for the other two reflections as "an exercise for the reader." Patrick Weisbecker wrote: Hi all, As a new rietveld user (fullprof) i wanted to check structure factors calculated thanks to several others softwares : Lazy-Pulverix, Powdercell 1.0 and Carine Crystallography 3.1. And i was surprised to obtain significants differences. For instance for Nickel FCC, lazy-pulverix and fullprof give for 111,200,220 planes :70.4,65.2,50.3 but powdercell 1.0 and Carine Crystallography give for the same planes 82.2,77.0,62.1. (no thermal factors had been considered in both cases) Such differences can have a great influence for quantitative analysis. Does someone know where differences come from? Which software is the more reliable? Patrick Weisbecker Laboratoire de Science et Genie des Materiaux metalliques Ecole des Mines de Nancy e-mail: [EMAIL PROTECTED] -- ******** Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
Re: looking for ICSD data...
Folks, I am bothered by the number of requests in the Rietveld is mailing list for copyright-protected data that I see crossing the ether. Particularly since most of the requested data comes out of the ICSD database. The ICSD database is available at a reasonable price to both industrial and academic users. [IMHO it is the only non-biological crystallographic database that can make that claim, with the possible exception of the NIST Crystal Data database :-)]. The ICSD is available for as little as 600 DM ($US 400) per year for individual academic users (see www.iucr.org). With nearly 50,000 structures, that is a lot of data for the money. I am sensitive to the fact that research money is tight. But compared to the costs of journals, books, x-ray tubes, travel, registration fees,... this is a pretty small cost. I suspect that most institutions can afford a copy of this database to put on a single PC, if not a copy on a intranet WWW server using the ILL software (as we do). If the data are freely traded on the web and only a few people buy the collection, the database will be exorbitant. If no one buys it, it will not be produced. I see this as both a matter of self-interest for the crystallographic community and one of scientific integrity. Brian Brian H. Toby, Ph.D.Leader, Crystallography Team [EMAIL PROTECTED] NIST Center for Neutron Research, Stop 8562 voice: 301-975-4297 National Institute of Standards Technology FAX: 301-921-9847Gaithersburg, MD 20899-8562
