[gmx-developers] t_CM_table in g_rdf

[David van der Spoel]

On 2010-04-24 13.58, Florian Dommert wrote:
>
> On 24.04.2010, at 13:46, David van der Spoel wrote:
>
>> On 2010-04-24 13.37, Florian Dommert wrote:
>>> Hello David,
>>>
>>> On 23.04.2010, at 18:17, David van der Spoel wrote:
>>>
>>>> On 2010-04-23 17.39, Florian Dommert wrote:
>>>>> Hello,
>>>>>
>>>>> I have a small problem with g_rdf. My aim is to determine the structure
>>>>> factor of an ionic liquid, but the problem is the t_CM_table in the
>>>>> gmx_rdf.c code. Only very few atomtypes are listed there and I do not
>>>>> really understand what the numbers mean. I have searched the mailing
>>>>> list and found a related question, but no answer was given.
>>>> Looks like a sum of Gaussians to me, that together make up the cross-section. I think you can find the numbers in the tables of crystallography (atomic scattering factors), however, these numbers are wavelength dependent. It would be good to put this kind of stuff in a data file. As a matter of fact I have been wanting to put all element properties into a single XML file, but this has to wait until we are past Gromacs 4.5.
>>>
>>> thanks for the immediate reply. So is there anything I can help to get g_rdf more flexible ? Perhaps we can provide a further option in g_rdf that reads the corresponding data from a simple txt file ? Afterwards the changes in the code and the switch to xml should not be much work ?
>>>
>> Yes that sounds reasonable. Just have the program (optionally) read a .dat file that contains the required numbers.
>
> Then I will pull the latest git-version and implement this feature.

Good.

Please remove the whole structure from the program and put the 
management of structure factors into separate .[ch] files. Something like:

typedef struct gmx_structurefactors *gmx_structurefactors_t;

extern gmx_structurefactors_t gmx_structurefactors_init(char *fn);

extern void gmx_structurefactors_done(gmx_structurefactors_t gsf);

extern int gmx_structurefactors_get_sf(gmx_structurefactors_t gsf,int 
elem,real a[4],real b[4],real c);

(check atomprop.h for comparison).

>
>>> Cheers,
>>>
>>> Flo
>>>
>>>>>
>>>>> Can anyone explain me what the numbers in the t_CM_table mean, so that I
>>>>> can enhance the table in the src code and make it applicable to further
>>>>> atoms.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Flo
>>>>>
>>>>>
>>>>> --
>>>>> Florian Dommert
>>>>> Dipl.-Phys.
>>>>>
>>>>> Institute for Computational Physics
>>>>>
>>>>> University Stuttgart
>>>>>
>>>>> Pfaffenwaldring 27
>>>>> 70569 Stuttgart
>>>>>
>>>>> Phone: +49(0)711/685-6-3613
>>>>> Fax: +49-(0)711/685-6-3658
>>>>>
>>>>> EMail: dommert at icp.uni-stuttgart.de<mailto:dommert at fias.uni-frankfurt.de>
>>>>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>>>> <http://fias.uni-frankfurt.de/~simbio/Florian_Dommert>
>>>>>
>>>>
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Dept. of Cell&   Molec. Biol., Uppsala University.
>>>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>>> --
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
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>>>
>>> --
>>> Florian Dommert
>>> Dipl.-Phys.
>>>
>>> Institute for Computational Physics
>>>
>>> University Stuttgart
>>>
>>> Pfaffenwaldring 27
>>> 70569 Stuttgart
>>>
>>> Phone: +49(0)711/685-6-3613
>>> Fax:   +49-(0)711/685-6-3658
>>>
>>> EMail: dommert at icp.uni-stuttgart.de
>>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>>>
>>>
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell&  Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-request at gromacs.org.
>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
>
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> Phone: +49(0)711/685-6-3613
> Fax:   +49-(0)711/685-6-3658
>
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se