[Smeagol-discuss] question about smeagol-run error
Awadhesh Narayan
narayaa at tcd.ie
Mon Jun 16 16:56:01 IST 2014
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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.tchpc.tcd.ie/pipermail/smeagol-discuss/attachments/20140616/f76895c3/attachment.html>
More information about the Smeagol-discuss
mailing list