TOPAS-Academic V7

2020-05-11 Thread alancoelho
Hi All Just letting everyone know that TOPAS-Academic Version 7 is now available. See where New7.PDF and the Technical_Reference.PDF can be downloaded. The Bruker-AXS version won't be far behind. Cheers Alan

RE: Software re-binned PD data

2019-09-26 Thread alancoelho
Hi Tony >My I ask is this re-bined data from the measurement software considered as "raw data" or "treated data"? I'm not sure what is meant by treated data. Almost all neutron data and synchrotron data with area detectors are "treated data". If the detector has a slit width in the

TOPAS Working on MACs

2019-03-04 Thread alancoelho
Hi all Some MACs users are experiencing problems using TOPAS/TOPAS-Academic on a MAC emulating windows. If you are using a successfully using TOPAS on a MAC then can you please send me a private e-mail with the details of your emulator; ie. is it Parallels Desktop, VMware Fusion, VirtualBox or

RE: Rietveld

2018-08-21 Thread AlanCoelho
It seems that even the origin of least squares is debateable: "That Gauss was the first to define the method of least squares was contested in his day. Adrien-Marie Legendre first published a version

RE: [Fwd: Question on file formats]

2008-12-11 Thread AlanCoelho
Lee Wrote I have some ToF data from GEM ISIS as both a .gss and a .asc file. I have managed to import and refine this using GSAS but am having some difficulties importing into TOPAS. Does anyone have some advice please on maybe file exchange or getting this file into the correct format to be read

RE: macro's in TOPAS

2008-12-04 Thread AlanCoelho
Hi Ross There's no way of outputting a selection of hkls; it's all or none. You can however omit hkls at the start of the refinement; ie. omit_hkls = And(H, K, Mod(L, 2)); omit_hkls = H 10; etc... You can use this in an indirect manner to first refine using all hkls

RE: Anisotropic peak broadening with TOPAS

2008-10-31 Thread AlanCoelho
Hi Frank I'm not 100% sure what you have been doing but I think the copying and pasting to get LVol values for particular sets of hkls can be maybe done in a more simple manner as shown below. If it's not clear then contact me off the list. prm lor_h00 300 min .3 prm lor_0k0 300 min .3

RE: PDF refinement pros and cons

2008-06-13 Thread AlanCoelho
Thanks all for the PDF explanations I think I'm beginning to understand. To summarise what we know: - PDF for powder data is a Patterson function (as Alan Hewat stated) in one dimension that plots the histogram of atom separation - It will show quite nicely the short range order and then

PDF refinement pros and cons

2008-06-12 Thread AlanCoelho
HI all Looking at the Pair Distribution Function and refinement I come away with the following: Fitting in real space (directly to G(r)) should be equivalent to fitting to reciprocal space except for a difference in the cost function. Is this difference beneficial in any way. In other

RE: Help: General spherical harmonics

2008-04-21 Thread AlanCoelho
Hi Xiujun Topas implements a normalized symmetrized sperical harmonics function, see Jarvine J. Appl. Cryst. (1993). 26, 525-531 The expansion is simply a series that is a function hkl values. The series is normalized

RE: Use fix or programmable slits for Rietveld analysis

2007-03-26 Thread AlanCoelho
Hi Maria Automatic Divergence Slits (ADS) illuminate different parts of the post monochromator as a function of 2Th. I am guessing but I think that the crystals are good enough not to change the intensity too much; this is my experience with Y2O23 in any case. At around 70 to 80 degrees 2Th

RE: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-24 Thread AlanCoelho
Vincent wrote: It is a step forward for F/OSS as it acknowledges that open-source code allows to spread a new method better than a closed source. As opposed to, filing a patent - since patents were originally developed to ensure that new methods be available to all. You are right in that open

RE: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-24 Thread AlanCoelho
One last reassuring word to the users of TOPAS - if I may No open source algorithm under any license comes close to equalling those as implemented in TOPAS and its academic counterpart. This status quo shall remain. In the event that commercial entities are locked out of journals then in the

RE: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-23 Thread AlanCoelho
Not sure what to make of all this Jon I am to believe that scientists prefer to mull over source code rather than pseudo code and mathematical descriptions. Anyone that knows just a little about software development would know that source code is the last thing that one wants to see. How many

RE: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-23 Thread AlanCoelho
Vincent In the original message of Michael Love (forwarded by Jon Wright) it clearly states: Although there are still some small problems, I think that this is a big step forward, and certainly an interesting read, if you are interested in FOSS and science. What does still some problems

RE: [Fwd: [ccp4bb] Nature policy update regarding source code]

2007-03-23 Thread AlanCoelho
update regarding source code] AlanCoelho wrote: Not sure what to make of all this Jon Don't shoot the messenger, I was surprised enough by it to forward it to the list. I guess they imply if you want to keep all implementation details secret you should be patenting instead of publishing

RE: Problems using TOPAS R (Rietveld refinement)

2007-03-21 Thread AlanCoelho
Clay people I think the single crystal analysis of clays is interesting. I have not read the literature but in determining the intensities is overlap of the dots considered as I would have expected the dots to be very much smeared (5 to 10 degrees 2Th in my experience). If yes the fitting in two

RE: Problems using TOPAS R (Rietveld refinement)

2007-03-21 Thread AlanCoelho
Lubo SVD as you mentioned does avoid numerical problems as does other methods such as the conjugate gradient method. SVD minimizes on the residuals |A x - b| after solving the matrix equation A x = b. I would like to point out however that errors obtained from the covariance matrix are an

RE: Problems using TOPAS R (Rietveld refinement)

2007-03-15 Thread AlanCoelho
Leandro Not sure what the purpose of your refinement is but if it's quantification then your results would probably be in error to a large extent. The references given by Alan Hewat and Lubo Smrcok is probably a good starting point. Data quality and model errors typically mean that atomic

RE: Powder Diffraction In Q-Space

2007-02-21 Thread AlanCoelho
Simon Billinge wrote: We can resolve the problem by setting 2pi=1! What school did you go to; thanks for the info. This issue of plotting data is one of those's non-issues drummed up by groups familar with one format but not in another; I would suggest that everyone should be familar with both

RE: Powder Diffraction In Q-Space

2007-02-21 Thread AlanCoelho
Whether a program has a button to display data as a function of 1/d or a button to take the square toor of intensities is trivial to the point of not being talked about much less setting up web sites to get opinions. The only point worth talking about is how a conversion from 2Th to 1/d is done

RE: CIF for Pyrrhotite 4C

2007-02-02 Thread AlanCoelho
Hi Doug You can add new setting in the file SGCOM5.CPP where entries are in the form of computer adapted symbols by Uri Shmueli, Acta Cryst. (1984). A40, 559-567. I am probably wrong but my guess for F12/d1 is FMCI1A000P2D003 where I used the a+b face-diagonal rotation matrix of 2D,

RE: About zero counts etc.

2006-10-13 Thread AlanCoelho
-Original Message-From: AlanCoelho [mailto:[EMAIL PROTECTED]Sent: 13 October 2006 22:30To: rietveld_l@ill.frSubject: RE: About zero counts etc. Hi Bill and others Why cant this question of zero counts be answered in a simple and practical manner. I hope to read Devinder Sivia's excellent

TOPAS-Academic version 4 now available

2006-10-11 Thread AlanCoelho
:// All the bestAlan Coelho

RE: XFit issue

2006-10-10 Thread AlanCoelho
Hi Sajeev In XFIT the values of the observed data points in the xdd file needs to be all greater than 1. Simply copy the xdd file into a spread sheet and set values less than 1 to 1. alan -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wednesday, 11 October

Re: CIF format for powder work

2006-07-12 Thread AlanCoelho
Pam, as the author of the INP format it was not my intention to make your life difficult. Maybe I am wrong but is it the case that we are now supposed to write into CIF more than just primary/raw data. This to me is not what was originally meant for CIF; non-primary data such as logical

Re: how to find out POLARISATION Factor

2006-05-31 Thread AlanCoelho
degrees and less however reduces the problem consdierably for the FCJ approach. cheers alan -Original Message- From: Larry Finger [mailto:[EMAIL PROTECTED] Sent: Wednesday, 31 May 2006 7:25 AM To: AlanCoelho wrote: I would like to conclude that to be critical of a method

RE: how to find out POLARISATION Factor

2006-05-31 Thread AlanCoelho
Title: Message The saga continues It has been brought to my attention that the fit.xy data I provided in a previous e-mail has misfits in the tails as seen in the following (blue is ray tracing, red is convolution): These misfits are due to how the ray tracing program calculates the