[Smeagol-discuss] question about smeagol-run error
joyce79928cc .
joyce79928 at gmail.com
Thu Jun 19 15:21:15 IST 2014
Dear:
I modified my compilation and used your input file to calculate on smeagol.
It works. but after one minute, the job will become a zombie, which means
the job is still calculation but there is no output.
I have checked the situation of the job and it shows the job have used 99%
CPU and 0.2 memory.
it seems normal, but there just still no output after two hours past.
have you ever seen this problem before?
thank you!
--
Best Regards
邱芳瑜 Chiou Fang Yu
國立成功大學 材料科學與工程學系碩一
MOBILE：0930287221(中華)
GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
2014-06-17 18:00 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
> No problem...let me know if you manage to get it working.
>
> Awadhesh
>
>
> On 17 June 2014 10:54, joyce79928cc . <joyce79928 at gmail.com> wrote:
>
>> Dear:
>>
>> thank you for your help...
>> I recognized maybe it is the error of my compilation.
>> again, I am appreciated greatly your help.
>>
>> --
>> Best Regards
>>
>> 邱芳瑜 Chiou Fang Yu
>> 國立成功大學 材料科學與工程學系碩一
>> MOBILE：0930287221(中華)
>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>
>>
>>
>> 2014-06-17 17:35 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>
>> I commented out the options to write bands and wavefunctions and it works
>>> for me. Could you check if it does for you?
>>> Attached are the input and output files.
>>>
>>> Awadhesh
>>>
>>>
>>> On 17 June 2014 10:11, joyce79928cc . <joyce79928 at gmail.com> wrote:
>>>
>>>> Dear:
>>>>
>>>> thanks for your a lot of help...
>>>>
>>>>
>>>> --
>>>> Best Regards
>>>>
>>>> 邱芳瑜 Chiou Fang Yu
>>>> 國立成功大學 材料科學與工程學系碩一
>>>> MOBILE：0930287221(中華)
>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>
>>>>
>>>>
>>>> 2014-06-17 17:09 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>>>
>>>> Hi,
>>>>>
>>>>> Can you send me the latest input and output files that you are using?
>>>>> I will try to run the system myself and see if I can get it to work.
>>>>>
>>>>> Awadhesh
>>>>>
>>>>>
>>>>> On 17 June 2014 08:28, joyce79928cc . <joyce79928 at gmail.com> wrote:
>>>>>
>>>>>> Dear:
>>>>>>
>>>>>> I have enlarged my unit cell six times and it still appears the
>>>>>> error.
>>>>>> I have found another solution on the website.(as below)
>>>>>>
>>>>>> http://lists.tchpc.tcd.ie/pipermail/smeagol-discuss/2007-September/000310.html
>>>>>> I reduce my basic set by using
>>>>>> PAO.BasisSize DZ
>>>>>> PAO.EnergyShift 200 meV
>>>>>> originally I use default value( 0.02Ry=272meV)
>>>>>> but the error still occur...
>>>>>> I don't know why and I really have no idea...
>>>>>>
>>>>>> hope to get your or somebody's respnse that can help me solve the
>>>>>> problem...!
>>>>>> thank you!
>>>>>>
>>>>>> --
>>>>>> Best Regards
>>>>>>
>>>>>> 邱芳瑜 Chiou Fang Yu
>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>> MOBILE：0930287221(中華)
>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2014-06-17 1:05 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>>>>>
>>>>>> Yes it seems to be alright. I would also suggest to sort the
>>>>>>> coordinates along z direction when using smeagol.
>>>>>>>
>>>>>>> Awadhesh
>>>>>>>
>>>>>>>
>>>>>>> On 16 June 2014 17:26, joyce79928cc . <joyce79928 at gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear :
>>>>>>>>
>>>>>>>> I was wondering that increasing the number of unit cells along z
>>>>>>>> to four times is just like below?
>>>>>>>> (the file attached is the animation for this unit cell)
>>>>>>>>
>>>>>>>> %block LatticeVectors # Lattice vectors in units of
>>>>>>>> LatticeConstant
>>>>>>>> 1.000 0.000 0.000
>>>>>>>> 0.000 1.000 0.000
>>>>>>>> 0.000 0.000 4.000
>>>>>>>> %endblock LatticeVectors
>>>>>>>>
>>>>>>>> AtomicCoordinatesFormat ScaledCartesian # How are the
>>>>>>>> coordinates scaled
>>>>>>>>
>>>>>>>> %block AtomicCoordinatesAndAtomicSpecies
>>>>>>>> 0.0000 0.0000 0.0000 1 Si
>>>>>>>> 0.5000 0.5000 0.0000 1 Si
>>>>>>>> 0.0000 0.5000 0.1250 1 Si
>>>>>>>> 0.5000 0.0000 0.1250 1 Si
>>>>>>>> 0.2500 0.2500 0.0625 1 Si
>>>>>>>> 0.2500 0.7500 0.1875 1 Si
>>>>>>>> 0.7500 0.2500 0.1875 1 Si
>>>>>>>> 0.7500 0.7500 0.0625 1 Si
>>>>>>>> 0.0000 0.0000 0.2500 1 Si
>>>>>>>> 0.5000 0.5000 0.2500 1 Si
>>>>>>>> 0.0000 0.5000 0.3750 1 Si
>>>>>>>> 0.5000 0.0000 0.3750 1 Si
>>>>>>>> 0.2500 0.2500 0.3125 1 Si
>>>>>>>> 0.2500 0.7500 0.4375 1 Si
>>>>>>>> 0.7500 0.2500 0.4375 1 Si
>>>>>>>> 0.7500 0.7500 0.3125 1 Si
>>>>>>>> 0.0000 0.0000 0.5000 1 Si
>>>>>>>> 0.5000 0.5000 0.5000 1 Si
>>>>>>>> 0.0000 0.5000 0.6250 1 Si
>>>>>>>> 0.5000 0.0000 0.6250 1 Si
>>>>>>>> 0.2500 0.2500 0.5625 1 Si
>>>>>>>> 0.2500 0.7500 0.6875 1 Si
>>>>>>>> 0.7500 0.2500 0.6875 1 Si
>>>>>>>> 0.7500 0.7500 0.5625 1 Si
>>>>>>>> 0.0000 0.0000 0.7500 1 Si
>>>>>>>> 0.5000 0.5000 0.7500 1 Si
>>>>>>>> 0.0000 0.5000 0.8750 1 Si
>>>>>>>> 0.5000 0.0000 0.8750 1 Si
>>>>>>>> 0.2500 0.2500 0.8125 1 Si
>>>>>>>> 0.2500 0.7500 0.9375 1 Si
>>>>>>>> 0.7500 0.2500 0.9375 1 Si
>>>>>>>> 0.7500 0.7500 0.8125 1 Si
>>>>>>>>
>>>>>>>> thank you!
>>>>>>>>
>>>>>>>> --
>>>>>>>> Best Regards
>>>>>>>>
>>>>>>>> 邱芳瑜 Chiou Fang Yu
>>>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>>>> MOBILE：0930287221(中華)
>>>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> 2014-06-16 23:59 GMT+08:00 joyce79928cc . <joyce79928 at gmail.com>:
>>>>>>>>
>>>>>>>> Dear:
>>>>>>>>>
>>>>>>>>> Thanks a lot!!!
>>>>>>>>> I will try!
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Best Regards
>>>>>>>>>
>>>>>>>>> 邱芳瑜 Chiou Fang Yu
>>>>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>>>>> MOBILE：0930287221(中華)
>>>>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2014-06-16 23:56 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>>>>>>>>
>>>>>>>>> Okay, you can try increasing the number of unit cells along z to
>>>>>>>>>> four times the primitive cell and then most likely it will get rid of this
>>>>>>>>>> error.
>>>>>>>>>>
>>>>>>>>>> To increase the cell only along one direction you can use one of
>>>>>>>>>> the visualization codes, for example xcrysden and then you can multiply
>>>>>>>>>> along any of the directions (for this you would need to convert the
>>>>>>>>>> coordinates to xsf format):
>>>>>>>>>>
>>>>>>>>>> http://www.xcrysden.org/doc/modify.html#__toc__13
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 16 June 2014 16:39, joyce79928cc . <joyce79928 at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Dear:
>>>>>>>>>>>
>>>>>>>>>>> yes, the error is the same.
>>>>>>>>>>> the files attached is my input(Si.long.fdf and Si.psf) and
>>>>>>>>>>> output(Si.out and output.out)
>>>>>>>>>>> I think maybe output.out is the error for my compiling.
>>>>>>>>>>>
>>>>>>>>>>> Can I ask a stupid question? How to increase the unit cell only
>>>>>>>>>>> along the transport direction (z)?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Best Regards
>>>>>>>>>>>
>>>>>>>>>>> 邱芳瑜 Chiou Fang Yu
>>>>>>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>>>>>>> MOBILE：0930287221(中華)
>>>>>>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 2014-06-16 22:27 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>>>>>>>>>>
>>>>>>>>>>> Is the error same as before? Can you also send the input and
>>>>>>>>>>>> output files?
>>>>>>>>>>>> By the way you need to increase the unit cell only along the
>>>>>>>>>>>> transport direction (z), although increasing it along other directions
>>>>>>>>>>>> should not really cause an error.
>>>>>>>>>>>> One more thing: the coordinates need to be sorted in increasing
>>>>>>>>>>>> order along z direction.
>>>>>>>>>>>>
>>>>>>>>>>>> Awadhesh
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 16 June 2014 15:10, joyce79928cc . <joyce79928 at gmail.com>
>>>>>>>>>>>> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Dear:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thank you for your reply.
>>>>>>>>>>>>> I enlarge my unit cell by changing my unit cell
>>>>>>>>>>>>>
>>>>>>>>>>>>> from
>>>>>>>>>>>>> %block LatticeVectors # Lattice vectors in units
>>>>>>>>>>>>> of LatticeConstant
>>>>>>>>>>>>> 0.500 0.500 0.000
>>>>>>>>>>>>> 0.500 0.000 0.500
>>>>>>>>>>>>> 0.000 0.500 0.500
>>>>>>>>>>>>> %endblock LatticeVectors
>>>>>>>>>>>>>
>>>>>>>>>>>>> AtomicCoordinatesFormat ScaledCartesian # How are the
>>>>>>>>>>>>> coordinates scaled
>>>>>>>>>>>>>
>>>>>>>>>>>>> %block AtomicCoordinatesAndAtomicSpecies
>>>>>>>>>>>>> 0.000 0.000 0.000 1 Si
>>>>>>>>>>>>> 0.250 0.250 0.250 1 Si
>>>>>>>>>>>>> %endblock AtomicCoordinatesAndAtomicSpecies
>>>>>>>>>>>>>
>>>>>>>>>>>>> to
>>>>>>>>>>>>> %block LatticeVectors # Lattice vectors in units
>>>>>>>>>>>>> of LatticeConstant
>>>>>>>>>>>>> 1.000 0.000 0.000
>>>>>>>>>>>>> 0.000 1.000 0.000
>>>>>>>>>>>>> 0.000 0.000 1.000
>>>>>>>>>>>>> %endblock LatticeVectors
>>>>>>>>>>>>>
>>>>>>>>>>>>> AtomicCoordinatesFormat ScaledCartesian # How are the
>>>>>>>>>>>>> coordinates scaled
>>>>>>>>>>>>>
>>>>>>>>>>>>> %block AtomicCoordinatesAndAtomicSpecies
>>>>>>>>>>>>> 0.000 0.000 0.000 1 Si
>>>>>>>>>>>>> 0.500 0.500 0.000 1 Si
>>>>>>>>>>>>> 0.000 0.500 0.500 1 Si
>>>>>>>>>>>>> 0.500 0.000 0.500 1 Si
>>>>>>>>>>>>> 0.250 0.250 0.250 1 Si
>>>>>>>>>>>>> 0.250 0.750 0.750 1 Si
>>>>>>>>>>>>> 0.750 0.250 0.750 1 Si
>>>>>>>>>>>>> 0.750 0.750 0.250 1 Si
>>>>>>>>>>>>> %endblock AtomicCoordinatesAndAtomicSpecies
>>>>>>>>>>>>>
>>>>>>>>>>>>> but it still appears the error.
>>>>>>>>>>>>> Is my way to changing the unit cell wrong?
>>>>>>>>>>>>> thank you!
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> Best Regards
>>>>>>>>>>>>>
>>>>>>>>>>>>> 邱芳瑜 Chiou Fang Yu
>>>>>>>>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>>>>>>>>> MOBILE：0930287221(中華)
>>>>>>>>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>>>>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2014-06-16 17:52 GMT+08:00 Awadhesh Narayan <narayaa at tcd.ie>:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The unit cell along transport direction is too short, so
>>>>>>>>>>>>>> there is an overlap to the next nearest cell. If you double the unit cell
>>>>>>>>>>>>>> along transport direction then it should be work. This is also mentioned in
>>>>>>>>>>>>>> the last three lines of silicon.out file.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Awadhesh
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 16 June 2014 10:32, joyce79928cc . <joyce79928 at gmail.com>
>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Dear:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I met some questions when I calculate Si using smeagol.
>>>>>>>>>>>>>>> my fdf input used is attached.(silicon.long.fdf)
>>>>>>>>>>>>>>> Pseudo-potential input I used also attached.(Si.psf)
>>>>>>>>>>>>>>> there's some output I get:
>>>>>>>>>>>>>>> first is silicon.out like attached.
>>>>>>>>>>>>>>> second is output.out attached also.
>>>>>>>>>>>>>>> I have confused for several days and I can't figure out
>>>>>>>>>>>>>>> what's the problem.
>>>>>>>>>>>>>>> hope there's somebody that can help me solve the problem.
>>>>>>>>>>>>>>> thanks
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Best Regards
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 邱芳瑜 Chiu Fang Yu
>>>>>>>>>>>>>>> 國立成功大學 材料科學與工程學系碩一
>>>>>>>>>>>>>>> MOBILE：0930287221(中華)
>>>>>>>>>>>>>>> GMAIL：joyce79928 at gmail.com <wisdom4640 at gmail.com>
>>>>>>>>>>>>>>> HOTMAIL：joyce79928 at hotmail.com <wisdom4640 at hotmail.com>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Smeagol-discuss mailing list
>>>>>>>>>>>>>>> Smeagol-discuss at lists.tchpc.tcd.ie
>>>>>>>>>>>>>>> http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Awadhesh Narayan
>>>>>>>>>>>>>> Computational Spintronics Group.
>>>>>>>>>>>>>> School of Physics,
>>>>>>>>>>>>>> Trinity College, Dublin 2, Ireland.
>>>>>>>>>>>>>> Phone: 353-1-8968455
>>>>>>>>>>>>>> https://sites.google.com/site/awadheshnarayan00/
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> Awadhesh Narayan
>>>>>>>>>>>> Computational Spintronics Group.
>>>>>>>>>>>> School of Physics,
>>>>>>>>>>>> Trinity College, Dublin 2, Ireland.
>>>>>>>>>>>> Phone: 353-1-8968455
>>>>>>>>>>>> https://sites.google.com/site/awadheshnarayan00/
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Awadhesh Narayan
>>>>>>>>>> Computational Spintronics Group.
>>>>>>>>>> School of Physics,
>>>>>>>>>> Trinity College, Dublin 2, Ireland.
>>>>>>>>>> Phone: 353-1-8968455
>>>>>>>>>> https://sites.google.com/site/awadheshnarayan00/
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Awadhesh Narayan
>>>>>>> Computational Spintronics Group.
>>>>>>> School of Physics,
>>>>>>> Trinity College, Dublin 2, Ireland.
>>>>>>> Phone: 353-1-8968455
>>>>>>> https://sites.google.com/site/awadheshnarayan00/
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Awadhesh Narayan
>>>>> Computational Spintronics Group.
>>>>> School of Physics,
>>>>> Trinity College, Dublin 2, Ireland.
>>>>> Phone: 353-1-8968455
>>>>> https://sites.google.com/site/awadheshnarayan00/
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Awadhesh Narayan
>>> Computational Spintronics Group.
>>> School of Physics,
>>> Trinity College, Dublin 2, Ireland.
>>> Phone: 353-1-8968455
>>> https://sites.google.com/site/awadheshnarayan00/
>>>
>>>
>>
>
>
> --
> Awadhesh Narayan
> Computational Spintronics Group.
> School of Physics,
> Trinity College, Dublin 2, Ireland.
> Phone: 353-1-8968455
> https://sites.google.com/site/awadheshnarayan00/
>
>
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