[RMCProfile-users] RMCPROFILE
Henrik Mauroy
hmauroy at gmail.com
Fri May 9 14:14:05 BST 2014
Dear Benoit.
Could you please inform the email list how things go? Use an informative
topic for the email next time;)
I would also like to work on my x-ray PDFs and/or include them when
running neutron data obtained at GEM. So far I haven't had time yet. I'm
sure several others would also like to hear your comments, and about
your eventual success with your data.
Best,
Henrik
On 09.05.2014 13:37, Benoit Baptiste wrote:
> Dear Helen,
>
> Thank you very much for these very useful informations.
> I will try as soon as possible.
> I'm also happy to read that a new version is coming soon !
>
> sincerely,
>
> B. Baptiste
>
>
> helen.playford at stfc.ac.uk a ?crit?:
>
>> Dear Benoit,
>>
>> Thanks for your email. Here is some more information about using
>> RMCProfile with X-ray data. I am working on an example to show how it
>> works for the next release of the program (coming soon!) which will
>> hopefully clear things up further.
>>
>> To fit an X-ray F(Q) you can use the XRAY_RECIPROCAL_SPACE_DATA
>> keyword. The datafile that you use must contain the X-ray form
>> factors and the data itself must be convolved with the box size.
>> There is a program called xray_to_rmc included with RMCProfile that
>> will take data in the 'normal' rmc format, which is a two column
>> ascii starting with the number of data points, like so:
>>
>> 1200
>> #title line
>> x1 y1
>> x2 y2
>> . .
>> . .
>> xn yn
>>
>> and make a correctly formatted X-ray data file.
>>
>> Currently an X-ray PDF can be treated like a neutron PDF but with
>> different weightings. This is obviously an approximation and it's
>> important to fit the F(Q) and Bragg (if applicable) as well.
>>
>> So for an X-ray PDF you use the NEUTRON_REAL_SPACE_DATA keyword, and
>> supply a subordinate keyword NEUTRON_COEFFICIENTS which defines the
>> weightings. These you calculate in the same way as for neutrons but
>> replace the scattering length, b, with atomic number of the element
>> in question.
>>
>> I hope this answers your query but please do get in touch if not or
>> if you have further questions.
>>
>> Best wishes,
>> Helen
>>
>>
>>
>> From: rmcprofile-users
>> [mailto:rmcprofile-users-bounces at rmcprofile.org] On Behalf Of Benoit
>> Baptiste
>> Sent: 05 May 2014 08:52
>> To: rmcprofile-users at rmcprofile.org
>> Subject: Re: [RMCProfile-users] RMCPROFILE
>>
>> Dear Helen,
>>
>> I'm also working with x-ray PDFs (obtained with pdfgetx3 from Ag
>> source measurements) and I've read there is maybe a way to use it in
>> rmc profile. If it's possible, could you please give me more details
>> about that ? I didn't find anything in the manual...
>>
>> Thanks in advance,
>>
>> Benoît Baptiste
>>
>>
>>
>> --
>>
>> Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie
>>
>> Plateforme de diffraction des rayons X
>>
>> 4 Place Jussieu - case courrier 115
>>
>> 75005 Paris
>>
>>
>> Le 28/04/2014 13:22,
>> helen.playford at stfc.ac.uk<mailto:helen.playford at stfc.ac.uk> a écrit :
>> Dear H.Wu,
>>
>> Thank you for your email.
>>
>> The keyword XRAY_RECIPROCAL_SPACE_DATA should work (but requires the
>> data to be in a very specific format, which we are working on an
>> example for), but at the present time the keyword
>> XRAY_REAL_SPACE_DATA is not implemented as there are questions over
>> the accuracy of the Fourier transform. There are ways around this if
>> you need to work with X-ray PDFs, which I can explain in more detail
>> if necessary. Keywords with X_ at the start are not implemented.
>>
>> I am a little confused by your second paragraph. Do you have data
>> from SiO2? In SiO2 each Si is coordinated to four, not five O atoms.
>> The neighbour list file you show is telling you that some atoms do
>> not have the expected number of neighbours. If you were trying to run
>> with the SiO2 polyhedral restraint this would have caused the errors.
>> How did you generate the second file? It would not have produced
>> errors as each Si atom has 4 neighbours, but it's important that the
>> connectivity is correct (i.e. that Si atom #1 is really connected to
>> O atoms #65, 74, 79 and 85).
>>
>> Please let me know if you would like further help working with X-ray
>> data, or if you have any other questions.
>>
>> Best wishes,
>> Helen
>>
>> From: rmcprofile-users
>> [mailto:rmcprofile-users-bounces at rmcprofile.org] On Behalf Of ????
>> Sent: 22 April 2014 08:07
>> To: rmcprofile-users
>> Subject: [RMCProfile-users] RMCPROFILE
>>
>> Dear author ,
>>
>> I 'm working with local atomic arrangement in disorder
>> materials. When I study the RMCProfile software, I have some
>> questions so need your help.
>>
>> In the SF6 example, I can get better results after studying the
>> manual. But for the rmcsf6.dat file, I have some questions on the
>> keyword of "NEUTRON_REAL(or RECIPROCAL)_SPACE_DATA". If I have X-ray
>> diffraction data, I will modify "NEUTRON" to "XRAY", but there will
>> be some errors; but if I modify "NEUTRON" to "X", then it will
>> success, but there is no important "rmcsf6_PDF1.csv" and
>> "rmcsf6_SQ1.csv" files in the makefiles. I don't know the reason.
>>
>> Another question is restraint files. In the SF6 example, a S
>> atom is adjacent with six O atoms and a O atom is adjacent with one S
>> atom, because SF6 is unlinked octahedral material. When I research
>> SiO2, SiO2 is linked tetrahedral material, so there exists boundary
>> problem. In principle, a Si atom is adjacent with five O atoms and a
>> O atom is adjacent with two Si atom. But when I use
>> neighbour_list.exe to create restraint files, SiO2.sio is:
>> 64
>> 1 1 65
>> 2 2 66 80
>> 3 2 67 73
>> 4 2 68 79
>> 5 4 67 69 76 78
>> 6 4 65 73 79 80
>> 7 4 66 71 72 77
>> 8 4 68 70 74 75
>> 9 1 81
>> 10 4 69 74 82 96
>> 11 2 83 89
>> 12 2 84 95
>> 13 4 83 85 92 94
>> 14 4 81 89 95 96
>> 15 4 82 87 88 93
>> 16 4 84 86 90 91
>> 17 1 97
>> 18 2 98 112
>> 19 4 71 75 99 105
>> 20 2 100 111
>> 21 4 99 101 108 110
>> 22 4 97 105 111 112
>> 23 4 98 103 104 109
>> 24 4 100 102 106 107
>> 25 2 70 113
>> 26 4 101 106 114 128
>> 27 4 87 91 115 121
>> 28 2 116 127
>> 29 4 115 117 124 126
>> 30 4 113 121 127 128
>> 31 4 114 119 120 125
>>
>> But there is error when I run the RMCProfile. I artificially change
>> SiO2.sio file to SF6-like restraint files, there is no error. I don't
>> know the reasons.This is modified file:
>> 64
>> 1 4 65 74 79 85
>> 2 4 66 80 87 92
>> 3 4 67 73 78 86
>> 4 4 68 79 81 91
>> 5 4 67 69 76 78
>> 6 4 65 73 79 80
>> 7 4 66 71 72 77
>> 8 4 68 70 74 75
>> 9 4 81 88 93 99
>> 10 4 69 74 82 96
>> 11 4 83 89 98 116
>> 12 4 84 95 97 102
>> 13 4 83 85 92 94
>> 14 4 81 89 95 96
>> 15 4 82 87 88 93
>> 16 4 84 86 90 91
>> 17 4 97 99 105 116
>> 18 4 98 112 128 134
>> 19 4 71 75 99 105
>> 20 4 100 111 147 158
>> 21 4 99 101 108 110
>> 22 4 97 105 111 112
>> 23 4 98 103 104 109
>> 24 4 100 102 106 107
>> 25 4 70 113 139 178
>> 26 4 101 106 114 128
>> 27 4 87 91 115 121
>> 28 4 116 127 178 175
>> 29 4 115 117 124 126
>> 30 4 113 121 127 128
>> 31 4 114 119 120 125
>>
>> I know my expression have some questions, so I'm very sorry and hope
>> you forgive me. Thank you very much!
>>
>> Best wish!
>>
>> H.Wu
>>
>>
>> --
>> Scanned by iCritical.
>>
>>
>>
>>
>>
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