[RMCProfile-users] get_gsas_bragg
Tucker, Matthew G.
tuckermg at ornl.gov
Sun Dec 15 21:55:11 GMT 2019
Dear Bob and Martin,
It is great we you are both working on GSAS-II integration with RMCProfile. When I coded the bragg part over 15 years ago now, I took my lead from GSAS-I and its manual. At the time I checked that RMCProfile could reproduce the output from GSAS-I for the first three GSAS time-of-flight functions #1, #2 and #3, to the point where the difference was negligible for "perfect" models (i.e zero UISO). It was never intended to have the functionality of GSAS, the aim was always to use GSAS for Rietveld/Bragg calculations and then use that information (Profile, background and Scale), leaving RMC to just calculate the bragg intensities from the models. At that time it certainly did a good enough job to be able to use the Bragg profile as a data constraint, at least for the test cases. Obviously bugs could have crept in, since the code has been through a lot since then.
Bob: How "incorrect" is the profile #3 in RMCProfile and if you let me know what is wrong we will get it fixed, not sure I have used function #3 recently.
To help avoid this in the future we have been trying a new approach to working with Rietveld programs. The idea is to get the Rietveld program to calculate the profile functions and write them out, then RMCProfile uses this directly. This has the advantage that the functions are hopefully guaranteed to match, since the same code is producing them, any new features/functions/bug-fixes in the Rietveld program can be used, and the information can then also be used to provide a resolution correction for the S(Q) and PDF data. Yuanpeng has coded this up and it will be available in the next version 6 release.
There are several replacements for the plotting in the works but it is great that GSAS-II will be able to do this and make RMCProfile more accessible for GSAS-II users. When do you think this will be available in the release version of GSAS-II, or is it there as you are developing it?
The need for matching filenames will go away in version 7 of RMCProfile, although this does put extra bookkeeping on the users but brings more flexibility and makes integration with other programs and GUIs more straight forward.
Martin: Which main version of RMCProfile are you talking about 6 or 7? If 6 it is probably there now (Yuanpeng please can you confirm), if 7 then we are working on getting the tutorial files and some examples ready before we upload a beta version to the download site.
Best wishes,
Matt
On 12/15/19, 2:48 PM, "rmcprofile-users on behalf of Von Dreele, Robert B." <rmcprofile-users-bounces at shadow.nd.rl.ac.uk on behalf of vondreele at anl.gov> wrote:
Dear Martin,
You should make sure you use the most recent version of GSAS-II for
this. I'm not done yet. & I found a miscoding of the Chebyschev
background function in GSAS-II. This is now fixed but you "must" use
background function "chebyschev-1" for RMCProfile. There is also a
problem with the GSAS profile function #3; I'll be trying to sort that
out this week; RMCProfile doesn't calculate the correct profiles. What
is also nice is that GSAS-II will execute RMCProfile and is able to
retrieve data & plot it as it is running. (NB: that completely replaces
the pgplot routine (rmcplot). The snag at present is that the 'run.dat'
file name must match those of the e.g. .bragg file. I hope to have
GSAS-II make the run file as well; it's a bit trickier.
Best,
Bob
On 12/15/2019 12:36 PM, Martin Dove wrote:
> It is true, GSAS 1 is now only ok for Windows users.
>
> There is good news for RMCprofile and GSAS 2. That is that GSAS 2 now produces a single file for each data bank that includes the Bragg profile, the background as a per-point value, all the instrument parameters for that data bank, and the scale factor for the bank. This means that there is no need to use data2config to generate .bragg, .back or .inst from the GSAS files because this new output file replaces them all.
>
> In short, so much nicer :)
>
> RMCprofile has been updated to read in these files, but Matt or someone can say whether this is now in the distributed version.
>
> Best wishes
>
> Martin
>
>
>> On 10 Dec 2019, at 18:44, Von Dreele, Robert B. <vondreele at anl.gov> wrote:
>>
>> Hi Matt,
>>
>> NB: the old gsas will not run on the most recent version of OSX. Apple
>> no longer provides the 32-bit libraries that gsas requires & gsas can
>> not be compiled successfully in 64-bits because it uses 32-bit pointers
>> in genles.
>>
>> Bob
>>
>> On 12/10/2019 4:29 PM, Tucker, Matthew G. wrote:
>>> Hi Victor,
>>>
>>> Please can you send me a file list of the directory you are working in with the ‘ls -l’ command.
>>>
>>> Also please can you run data2config on the .TBL file you have produce and send me a copy of its output.
>>>
>>> The error on the mac looks like it is try to run gsas but you don’t have a copy in /Application/gsas/exe
>>>
>>> On windows it looks like there is a problem with the .hst file and finding the bragg data you should have written to the .LST file in stage 5 of the Appendix A instructions. Unfortunately the order you do things does matter, so if gsas has been run since your ran hstdmp you will need to run it again and to be safe it is probably best to move the existing .LST file or delete it if you don’t need it.
>>>
>>> It is better to use data2config if you can prepare your files ahead of time, if not get_gsas_bragg can run gsas for you but it is older and doesn’t always work depending on how the files are setup.
>>>
>>> Best wishes,
>>> Matt
>>>
>>> From: Changhao Zhao <czhao1021 at outlook.com>
>>> Date: Tuesday, December 10, 2019 at 8:59 AM
>>> To: "Poree Victor Alexis (PSI)" <victor.poree at psi.ch>, "rmcprofile-users at shadow.nd.rl.ac.uk" <rmcprofile-users at shadow.nd.rl.ac.uk>
>>> Subject: Re: [RMCProfile-users] get_gsas_bragg
>>>
>>> Hi Victor,
>>>
>>> Actually, I have encountered the same problem as yours. An alternative solution is to edit the .bragg file manually. You can refer to the format of the .bragg file in the RMCProfile manual. Then extract each data point of your XRD pattern, and output a .bragg file containing all the data points (this can be easily done by MATLAB). Hope this helps you.
>>>
>>> Best,
>>> Changhao
>>> ________________________________
>>> From: rmcprofile-users <rmcprofile-users-bounces at shadow.nd.rl.ac.uk> on behalf of Poree Victor Alexis (PSI) <victor.poree at psi.ch>
>>> Sent: Tuesday, December 10, 2019 1:05 PM
>>> To: rmcprofile-users at shadow.nd.rl.ac.uk <rmcprofile-users at shadow.nd.rl.ac.uk>
>>> Subject: Re: [RMCProfile-users] get_gsas_bragg
>>>
>>> Hello,
>>>
>>> That's what I used to get the .back, .inst etc. But it did not generate a .bragg.
>>>
>>> Best,
>>>
>>> Victor
>>>
>>> On 10.12.19, 12:53, "rmcprofile-users on behalf of Martin Dove" <rmcprofile-users-bounces at shadow.nd.rl.ac.uk on behalf of martin.dove at qmul.ac.uk> wrote:
>>>
>>> Why don’t you use data2config to do it?
>>>
>>> Best wishes
>>>
>>> Martin
>>>
>>>> On 5 Dec 2019, at 16:47, Poree Victor Alexis (PSI) <victor.poree at psi.ch> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I am setting up the starting files to begin my RMCProfile simulation.
>>>>
>>>> I have used GSAS to fit the data (obtained on GEM) under windows (the Mac version is not cooperating). I have generated the .back, .inst etc using the RMCProfile tools. However I cannot obtain the .bragg. I tried using the get_gsas_bragg command but I get the following errors in both Mac and windows (see attachment).
>>>>
>>>> What should I do to solve this and get starting with the RMC?
>>>>
>>>> Best regards,
>>>>
>>>> Victor Porée
>>>> ----------------------------
>>>> Laboratory for Neutron Scattering and Imaging (LNS)
>>>> Paul Scherrer Institut
>>>> WHGA 142
>>>> Forschungsstrasse 111
>>>> 5232 Villligen PSI
>>>> Phone: +41 56 310 36 23
>>>> victor.poree at psi.ch<mailto:victor.poree at psi.ch>
>>>>
>>>>
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