[Smeagol-discuss] problem with the bulk calculation

[Ivan Rungger]

Dear Tao,

   as you write the leads calculation can only be done in serial. First
I would set MullikenInSCF to False, so that you avoid printing the
mulliken population at each step. Then please rerun the leads
calculation with both smeagol and siesta (the bare siesta1.3 without the
smeagol part) on one node, so that we see if it is a smeagol or siesta
problem. Can you then please send both output files, I will then have a
look at them and test them?

Cheers,

 Ivan

Tao K wrote:
> Dear Salvador,
>
> Now, I know the program suspends after the "transport is along the
> z-direction" notice is caused by the parallel calculations. When I want
> to run the program in serial(with only one processor), however, it
> suspends at the beginning (after Being MD step = 1), and I find the average load of the CPU is more than 200%. 
>
> Could anyone give me some advices? Thanks a lot.
>
> Best wishes,
> Kun Tao
>
>
> Salvador Barraza-Lopez wrote:
>   
>>  Dear Tao,
>>
>>  I don't know about the following part:
>>
>> siesta: Mulliken populations before mixing
>> siesta: Mulliken populations before mixing
>> siesta: Mulliken populations before mixing
>> siesta: Mulliken populations after mixing
>> siesta: Mulliken populations after mixing
>> siesta: Mulliken populations after mixing
>>
>>  I have noticed the same issue you report. The hanging of the program
>> after the "transport is along the z-direction" notice. I assume you
>> are running the leads (bulk) calculation in parallel (more than 1
>> processor). I have to run that part using a single processor.
>> Hopefully your leads are not extremely big.
>>
>>  Best regards,
>> Salvador.
>>
>> On Tue, 5 Feb 2008, Tao K wrote:
>>
>>     
>>> Dear Smeagol user,
>>>
>>> When I was trying to use Smeagol for bulk calculation ( Au(001)surface
>>> ), the program finished the siesta part but ended with:
>>>
>>> "The transport is along the z direction"
>>>
>>> However, there were no *.HST, bulklft.DAT and bulkrgt.DAT files. So I
>>> couldn't use them for transmission calculations.
>>>
>>> Moreover, in the output file, I found some strange information,such as:
>>> siesta:   10   -36504.4537   -36508.4626   -36508.7272  0.0297 -3.4303
>>> siesta: Mulliken populations before mixing
>>> siesta: Mulliken populations before mixing
>>> siesta: Mulliken populations before mixing
>>> siesta: Mulliken populations after mixing
>>> siesta: Mulliken populations after mixing
>>> siesta: Mulliken populations after mixing
>>> siesta:   11   -36504.4385   -36504.4214   -36504.6860  0.0001 -3.4005
>>>
>>> I used smeagol1.0b and siesta-1.3flp and had patch the smeagol with
>>> patch-flp-0b-1.patch.  Could anyone give me advices? Thanks a lot.
>>>
>>> Attached below are my arch.make and output files.
>>>
>>> Sincerely yours,
>>> Kun Tao
>>>
>>>
>>>       
>
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>   


-- 
=================================================
Ivan Rungger,

School of Physics,  
Trinity College Dublin,  
Dublin 2,  IRELAND  
Phone: +353-1-6088454  
Email: runggeri at tcd.ie

=================================================