[gmx-developers] iparams size question

[francesco oteri]

So, in iparams there are non-bonded parameters + bonded,
that is (atnr² + bonded) number of entryes, am I right?

Francesco

2013/4/7 David van der Spoel <spoel at xray.bmc.uu.se>

> On 2013-04-06 20:19, Mark Abraham wrote:
>
>>
>>
>> On Sat, Apr 6, 2013 at 7:52 PM, francesco oteri
>> <francesco.oteri at gmail.com <mailto:francesco.oteri at gmail.**com<francesco.oteri at gmail.com>>>
>> wrote:
>>
>>     Dear gromacs developers,
>>     on the webpage describing the data sructures
>>     (http://www.gromacs.org/**Developer_Zone/Programming_**
>> Guide/Data_Structures<http://www.gromacs.org/Developer_Zone/Programming_Guide/Data_Structures>
>> )
>>     it is written that "t_iparams *iparams; ///matrix of size atnr² with
>>     interaction params"/
>>
>>
>>     but looking at the different part of the code (ex pr_iparams in
>>     txtdump.c) it is clear that in iparams there are all the parameters
>>     for the possible nteractions, so for sure is more than atnr**2 and
>>     it seems to me that the size should be ntypes.
>>
>>     Am I wrong?
>>
>>
>> Probably not. The code is definitive. The size of a matrix is whatever
>> it was given when it was allocated. A comment is a doubtful secondary
>> source of information. A webpage is even less likely to be definitive :-)
>>
>> That programming guide was contributed by a user some years ago, and
>> AFAIK could have any sort of inaccuracies. One of the lessons of history
>> is that documentation that is not in the code does not get maintained
>> when the code changes. For 5.0, there are plans to a) document better,
>> and b) make that available via Doxygen.
>>
>
> The comment applies to the matrix of non-bonded parameters (LJ or
> Buckingham) which is the square of the number of atomtypes. On top of that
> there are the bonded interactions.
>
>>
>> Mark
>>
>>
>>     Francesco
>>
>>     --
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>> >.
>>
>>
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
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-- 
Cordiali saluti, Dr.Oteri Francesco
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