[gmx-developers] How to collect coordinates in parallel version?

[Mark Abraham]

On 16/06/2011 5:46 PM, Rene Staritzbichler wrote:
> Hi Mark,
>
> Is it this one?:
>
> dd_move_x(cr->dd,box,x);

No. See write_traj() in src/mdlib/stat.c

Mark

>
> Thanks, Rene
>
>
>
>
> On 06/15/2011 12:09 AM, Mark Abraham wrote:
>> On 15/06/2011 12:56 AM, Rene Staritzbichler wrote:
>>> Dear developers,
>>>
>>> I tried to implement a simple little feature in Gromacs 4.5. that 
>>> needs to write the coordinates of all atoms into a file. I failed to 
>>> write them in the order which the non-parallel version prints.
>>
>> There's code that collects coordinates before writing trajectory 
>> files. Use that.
>>
>> Mark
>>
>>> From what I understand I need to translate the global into the local 
>>> indices, which is done with
>>> cr->dd->ga2la[global_index].a
>>>
>>> I call a function from sim_util.c after the 'do_flood' call.
>>> Somehow I cannot access the ga2la correctly.
>>> Do I need to include other files than 'domdec.h' or 'gmx_ga2la.h'?
>>>
>>> Best,
>>>
>>> Rene Staritzbichler
>>>
>>> Max Planck Insitute of Biophysics
>>> Max von Laue Str. 3
>>> 60438 Frankfurt
>>>
>>>
>>>
>>>
>>