Thanks Dr. Matteo. That is helpful.<br><br><div class="gmail_quote">On Tue, Jul 10, 2012 at 11:15 AM, Matteo Cococcioni <span dir="ltr"><<a href="mailto:matteo@umn.edu" target="_blank">matteo@umn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Peng,<br>
<br>
let me add one word to Burak's.<br>
you need to distinguish two O kinds anyway, whether you shift the<br>
atomic position or not. if you don't do that you will be perturbing<br>
all the oxygen atoms at the same time.<br>
The necessity to have the perturbed atom described as of a different<br>
type (although with the same pseudopotential) is what makes it<br>
convenient (most of the time) to place it at the origin of the unit<br>
cell.<br>
<br>
best,<br>
<br>
Matteo<br>
<div class="im HOEnZb"><br>
<br>
<br>
On Tue, Jul 10, 2012 at 10:03 AM, Peng Chen <<a href="mailto:pchen@ion.chem.utk.edu">pchen@ion.chem.utk.edu</a>> wrote:<br>
</div><div class="HOEnZb"><div class="h5">> When O is perturbed in the case of NiO in tutorial, it is re-positioned and<br>
> there are 2 different kinds of O (first with 1 atom, the second with 7<br>
> atoms). Then the kind with only one O is perturbed. In the tutorial, it<br>
> reads "This is done to preserve the largest possible number of symmetries".<br>
> Is this process necessary? Can we just run computation without re-position?<br>
> In that case, there is only one kind of O with 8 atoms.<br>
><br>
> In the position file "filepos", the scale of cell length is always 10, even<br>
> if the scale is 7.9 in NiO and 5.42 in Fe. Shall we always use 10 in<br>
> position file no matter what the real scale is?<br>
><br>
> On Tue, Jul 10, 2012 at 9:37 AM, Burak Himmetoglu <<a href="mailto:himm0013@umn.edu">himm0013@umn.edu</a>> wrote:<br>
>><br>
>> Hi Peng,<br>
>><br>
>> r.x assigns the values of the response matrices only by considering the<br>
>> distance between atoms and whether they have the same spin and type or not.<br>
>> This information has to be given by the user in the positions file "filepos"<br>
>> read by &input_mat. If B(1) and B(2) are different types<br>
>> (e.g. crystallographically) you should perturb them separately, as you<br>
>> outlined in the procedure, and make sure that ntyp=3 (type 1 is B(1), type 2<br>
>> is B(2) and type 3 is O) in the namelist &input_mat that goes into r.x<br>
>><br>
>> Best regards,<br>
>><br>
>> Burak<br>
>><br>
>><br>
>> On Tue, Jul 10, 2012 at 1:45 AM, Stefano de Gironcoli <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>><br>
>> wrote:<br>
>>><br>
>>> I don't know the details of r.x code but I think that, physically, what<br>
>>> matters is the two atoms are crystallographically equivalent or not<br>
>>> .therefore I think space group symmetry is the relevant one.<br>
>>><br>
>>> stefano<br>
>>><br>
>>><br>
>>> On 07/10/2012 05:54 AM, Peng Chen wrote:<br>
>>><br>
>>> Dear All,<br>
>>><br>
>>> In the calculation of U, how can we determine the equivalence of the<br>
>>> ions,<br>
>>> by site symmetry or space group symmetry?<br>
>>> E.g ABO3, B ions has 2 different site symmetries (B(1) B(2)). Shall we<br>
>>> run<br>
>>> calculation on perturbing B(1) and B(2) ions or just a B ion?<br>
>>><br>
>>> In order to find U in B ions, I tried to run calculation with<br>
>>> perturbing<br>
>>> just on B, and r.x gave some errors that it needs to read more data.<br>
>>> So I guess it needs the perturbed data from other atoms. Shall I use the<br>
>>> procedures listed below?<br>
>>> 1. run scf calculation with Hubbard_U(i)= 1.d-20<br>
>>> 2. run scf with perturbing on an A ion<br>
>>> 3. run scf with perturbing on a B(1) ion<br>
>>> 4. run scf with perturbing on a B(2) ion<br>
>>> 5. run scf with perturbing on an O ion<br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
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><br>
><br>
><br>
> --<br>
> Best Regards.<br>
> Peng<br>
><br>
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--<br>
</div></div><span class="HOEnZb"><font color="#888888">Matteo Cococcioni<br>
Department of Chemical Engineering and Materials Science,<br>
University of Minnesota<br>
421 Washington Av. SE<br>
Minneapolis, MN 55455<br>
Tel. <a href="tel:%2B1%20612%20624%209056" value="+16126249056">+1 612 624 9056</a> Fax <a href="tel:%2B1%20612%20626%207246" value="+16126267246">+1 612 626 7246</a><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br> Best Regards.<br> Peng <br>