[RMCProfile-users] FW: [EXTERNAL] A question in RMCProfile
Zhang, Yuanpeng
zhangy3 at ornl.gov
Mon Nov 30 13:30:57 GMT 2020
Hi Andy,
I saw your email to the mailing list this morning concerning problems with data2config and stuff. I remember we had the discussion earlier so I am not sure whether your issue is still there. I attach our discussion below anyways and if you still have the issue, please feel free to let me know and we can discuss.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>
From: Zhang, Yuanpeng <zhangy3 at ornl.gov>
Date: Friday, November 27, 2020 at 9:51 AM
To: Chun Mann Chin <c.chin at sheffield.ac.uk>
Subject: Re: [EXTERNAL] A question in RMCProfile
Using cif file to generate rmc6f is just the same as using TBL file, command will be something like,
data2config -noannotate -order [All atom types go here] -supercell [Supercell dimension goes here] -rmc6f INPUT_FILE.cif
Those Bragg files can be obtained using ‘get_gsas_bragg’ – you should read RMCProfile tutorials first.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>
From: Chun Mann Chin <c.chin at sheffield.ac.uk>
Date: Friday, November 27, 2020 at 7:16 AM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov>
Subject: Re: [EXTERNAL] A question in RMCProfile
I agree that doing the transformation with CrystalMaker is much easier. However, once you get the .cif file, how can you convert it into a .rmc6f file? I am sorry but I don't know the command in data2config which allows me to change from .cif to .rmc6f file.
Moreover, I am curious that you don't have to use the .TBL file. From what I understand, I need the .EXP, .TBL and .LST files to extra .bragg, .back and .inst files etcc from the data2config function for the RMCProfile simulation. Therefore, I wonder if you mind sharing how you would have run the RMCProfile simulation from scratch (aka from the file I gave you)?
Sorry for asking a lot of questions but I am really interested in this program and I believe it is a very powerful tool!
Best wishes,
Andy
On Fri, 27 Nov 2020 at 05:05, Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>> wrote:
I strongly suggest you do the transformation into P1 with CrystalMaker. Assuming you have full occupancy for La and Ti as initially, then after transforming into P1, you can delete whichever atoms you want in the in the P1 unit cell. Then you can export CIF from there, which I think won’t cause any issues with data2config.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>
From: Chun Mann Chin <c.chin at sheffield.ac.uk<mailto:c.chin at sheffield.ac.uk>>
Date: Thursday, November 26, 2020 at 11:02 PM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>>
Subject: Re: [EXTERNAL] A question in RMCProfile
I am sorry but I don't seem to follow here. I have had a look at your .rmc6f files. For Crystal.rmc6f, if you were able to generate this file directly from data2config with just the .EXP, .TBL and .LST file, can you please let me know what your command line is? Mine is:
>data2config -rmc6f -noannotate -supercell[1 1 1] LLWO_300K.TBL
And I have the same error message no matter what size I try to make the supercell to be (ie [1 1 1] is the same as [10 10 7]).
On another note, if you have used my .TBL file which has 20 atoms in total, why are you have Va (Vacancy) atoms in the .rmc6f file? The reason I set it as P1 instead of P21/n, is to get rid of the vacancy atoms I am having. Although I agree that the total atoms in your Crystal.rmc6f is exactly the file I am looking for, I am a bit confused why you are having Vacancy atoms in it.
Best wishes,
Andy
On Fri, 27 Nov 2020 at 03:38, Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>> wrote:
I am not seeing any issues with the input and output structure. I was using your cmdx file to export cif and use data2config to generate rmc6f file.
Crystal.cif – CIF with particle occupancy.
Crystal.rmc6f – rmc6f generated accordingly. Number of atoms seems be correct considering the occupancy.
Crystal_Full.cif – CIF without occupancy.
Crystal_Full.rmc6f – rmc6f generated accordingly. Number of atoms seems to be correct.
Crystal_Full_new.rmc6f – a 1x1x1 ‘supercell’ (i.e. a unit cell) containing 24 atoms. Number of atoms is correct.
I cannot see any issues here. But if you want to generate a 1x1x1 ‘supercell’ as rmc6f format with data2config, there may be an ‘issue’ there – we have limited number of atoms for the program to randomly select sites to occupy, which may end up with some unexpected results. But it just does not make any sense to generate a unit cell with rmc6f format.
As for the same type of atoms sitting on different crystallographic sites, you can separate them in rmc6f file (i.e. you don’t want to put them next to each other) and RMCProfile can cope with this without problem.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>
From: Chun Mann Chin <c.chin at sheffield.ac.uk<mailto:c.chin at sheffield.ac.uk>>
Date: Thursday, November 26, 2020 at 10:09 PM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>>
Subject: Re: [EXTERNAL] A question in RMCProfile
Hi Yuanpeng,
Thanks for replying my email. This is actually my problem as I cannot generate a .rmc6f file from data2config. I have manually built a model from CrystalMaker as per some published data on the compound La1.5Li1.5WO6 (which I have now attached it as a .cmdx file). I have also attached a paper on this particular compound.
If you look at the structure information, you can see the occupancy for La and "Ti" (Li at the A site) are less than 1. This creates vacancy in the model. However, the CrystalMaker program doesn't do the shading sphere to reflect the occupancy issue. Instead, it shows a model as if both La and "Ti" have occupancy equal to 1. (Hence, you can see the "Ti" and La spheres are very close to each other).
My idea was to break this model into P1. In this case, I can then specify the positions of the La and "Ti" atoms, which in turns allow me to build the columnar ordering as indicated in the paper. However, as you can see from the .TBL file attached, I changed the model into P1 and yet and data2config program doesn't produce the .cif file and gives an error message instead. Helen Playford, who I worked with before, has found that RMCProfile sometimes cannot accommodate the same type of atom situated in more than one crystallographic site. As a result, I also replace the "duplicated" atoms with other elements to bypass this "bug". Yet, the result is the same. Therefore, I shall be extremely grateful if you could please take a look at it.
Many thanks and I am happy to discuss this further.
Best wishes,
Andy
On Fri, 27 Nov 2020 at 01:50, Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>> wrote:
Hi Andy,
Without seeing the input structure file you mentioned (I suppose you were using CIF format?), it is very hard for me to tell anything useful. Would you mind sharing with me your structure file so I can have a look?
Also, there is something on top of my head – if you are using cif file and do have access to CrystalMaker, it may be helpful to load the cif into crystalmaker and export the cif file from there. I know sometimes data2config cannot recognize some symmetry operations properly. This may not be the issue but just something to keep in mind.
Cheers
Yuanpeng
--
Dr. Yuanpeng Zhang
Computational Instrument Scientist
Spallation Neutron Source
Oak Ridge National Laboratory
1 bethel valley road, Oak Ridge, TN 37830, US
Mobile: +1(865)-335-4818
Email: zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov> | Web: https://www.iris2020.net<https://www.iris2020.net/>
From: Chun Mann Chin <c.chin at sheffield.ac.uk<mailto:c.chin at sheffield.ac.uk>>
Date: Thursday, November 26, 2020 at 3:21 PM
To: Zhang, Yuanpeng <zhangy3 at ornl.gov<mailto:zhangy3 at ornl.gov>>
Subject: [EXTERNAL] A question in RMCProfile
Hi Yuanpeng,
I have recently posted a question about RMCProfile but I have yet heard if it has been approved. I wonder if you could please help me out on this matter.
I was trying the data2config function for a crystal structure in P21/n space group. However, when I executed the function, the model generated from data2config only consists of 8 atoms while I should have 10 atoms instead.
I then tried to transform the model into P1 to accommodate the unusual cation ordering observed, and it should now have 20 atoms instead. I know it sounds silly, but I still ran the data2config. However, this time the following error message popped up:
forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read
Image PC Routine Line Source
data2config.exe 00007FF6F96AA908 Unknown Unknown Unknown
data2config.exe 00007FF6F96B04A5 Unknown Unknown Unknown
data2config.exe 00007FF6F959A34B Unknown Unknown Unknown
data2config.exe 00007FF6F9561A96 Unknown Unknown Unknown
data2config.exe 00007FF6F972A412 Unknown Unknown Unknown
data2config.exe 00007FF6F972A818 Unknown Unknown Unknown
KERNEL32.DLL 00007FF824807034 Unknown Unknown Unknown
ntdll.dll 00007FF8267DCEC1 Unknown Unknown Unknown
I then tried replace the same type of atoms with different elements (e.g. replace 2 Li with 1 Li and 1 Na, 2 W with 1 W and 1 Te etcc). Yet, I received the same error message. At the moment, I couldn't figure out what has/have gone wrong in my code. I shall be grateful if someone can provide some insights in this.
I am happy to discuss it further and thank you very much for your time!
Best wishes,
Andy
--
Dr Andy Chin
Department of Materials Science and Engineering
University of Sheffield
Sir Robert Hadfield Building
Mappin Street
Sheffield S1 3JD
01142 225510
--
Dr Andy Chin
Department of Materials Science and Engineering
University of Sheffield
Sir Robert Hadfield Building
Mappin Street
Sheffield S1 3JD
01142 225510
--
Dr Andy Chin
Department of Materials Science and Engineering
University of Sheffield
Sir Robert Hadfield Building
Mappin Street
Sheffield S1 3JD
01142 225510
--
Dr Andy Chin
Department of Materials Science and Engineering
University of Sheffield
Sir Robert Hadfield Building
Mappin Street
Sheffield S1 3JD
01142 225510
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