[RMCProfile-users] RMCPROFILE

Fri May 9 11:23:33 BST 2014

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.

_______________________________________________

rmcprofile-users mailing list

rmcprofile-users at rmcprofile.org<mailto:rmcprofile-users at rmcprofile.org>

http://lists.rmcprofile.org/mailman/listinfo/rmcprofile-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.rmcprofile.org/pipermail/rmcprofile-users/attachments/20140509/f6d78edd/attachment.html>