[RMCProfile-users] RMCPROFILE
Benoit Baptiste
Benoit.Baptiste at impmc.upmc.fr
Fri May 9 12:37:43 BST 2014
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
>
>
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