[gpaw-users] Fwd: Charged oxygen vacancy in periodic systems

Thu Mar 26 09:40:16 CET 2015

Hi,

On 03/25/2015 03:14 PM, Ask Hjorth Larsen wrote:
> Hello
>
> There is no fundamental incompatibility between using one
> pseudopotential for some atoms and another for other atoms, so you
> should be able to mix them.  However the HGH ones require much more
> fine grid spacing.
>
> The c_n, v_l and so on are lists of parameters for the HGH setups.
> They are described here:
> http://journals.aps.org/prb/abstract/10.1103/PhysRevB.58.3641
>
> The parameters are described in the beginning.  In the code, c_n are
> the coefficients of the local parts, while v_l is a list of
> "VNonLocal" objects that each correspond to a value of l, and some
> parameters that determine the non-local atomic part of the
> Hamiltonian.
>
> Unfortunately not a lot of tests have been done to compare HGH with
> PAW, as far as I know.
in a short time (order of a month) i'll be providing some comparisons.
What we know already now is that HGH pseudopotentials give incorrect 
atomization energies:
http://forum.abinit.org/viewtopic.php?f=9&t=1365

>    HGH is only used when people need to do
> "funny" stuff with the pseudopotentials, particularly testing things
> in a simpler way than with full PAW.  You are welcome to do a few
> comparisons.
>
> Note that if there's a semicore ('sc') HGH pseudopotential available,
> it's probably much better than the non-semicore one.
this is correct: semicore HGH are better than non-semicore.
Note that currently there is something in GPAW that makes
the HGH pseudopotentials results disagree with ESPRESSO/ABINIT in some 
cases..

Ask is looking into this problem.

Best regards,

Marcin

>
> Best regards
> Ask
>
> 2015-03-25 9:04 GMT+01:00 Teemu Parviainen <teemu.t.parviainen at student.jyu.fi>:
>> Hi,
>> Thank you for this information!
>>
>> I don't have any experience of generating and manipulating the setups. Also
>> I have used only paw setups in my earlier calculations so a couple of
>> questions arises:
>>
>> -How do you usually fiddle with all the parameters (c_n, v_l, rloc in this
>> case). I mean is there any basic scheme to change the parameters? What is
>> the criteria to accept the parameter set?
>>
>> -Is it OK to mix conventional paw setups with hgh setups (for example
>> defining hgh setups for Mg and paw for O)?
>>
>> -How do the results calculated with hgh and paw setups compare with each
>> other? For example, how do the calculated adsorption energies or vacancy
>> formation energies compare in general? Has anyone even studied this?
>>
>> Greetings,
>> -Teemu Parviainen, PhD student, Jyväskylä Finland
>>
>>
>>
>>
>> On 13 March 2015 at 12:43, Ask Hjorth Larsen <asklarsen at gmail.com> wrote:
>>> Hello
>>>
>>> Setups are extremely complicated, so if you fiddle with them it'll
>>> probably just result in garbage.  The HGH pseudopotentials are simple;
>>> you can create your own, providing/hacking a humane number of
>>> parameters.
>>>
>>> Grab the objects that encode the minimal set of parameters to specify
>>> the setup, and then improvise from there changing number of valence
>>> electrons, etc.:
>>>
>>>>>> from gpaw.hgh import setups
>>>>>> setups['Si']
>>> <gpaw.hgh.HGHParameterSet instance at 0x8cf798c>
>>>>>> dir(setups['Si'])
>>> ['Nv', 'Z', '__doc__', '__init__', '__module__', '__str__', 'c_n',
>>> 'configuration', 'copy', 'get_occupation_numbers', 'nl_iter',
>>> 'print_info', 'rloc', 'serialize', 'symbol', 'v_l', 'zeropad']
>>>
>>> Nv is valence electron number, c_n are coefficients, and v_l is a list
>>> of VNonLocal objects with info on the atomic Hamiltonian
>>> contributions.  Mix them however you like them and create a
>>> HGHParameterSet with that.  Then instantiate a HGHSetupData from that,
>>> and run your calculations with GPAW(setups={17: my_hghsetupdata}) to
>>> specify a custom setup for atom 17.
>>>
>>> Best regards
>>> Ask
>>>
>>>
>>> 2015-03-13 7:53 GMT+01:00 Ioannis Remediakis <remed at materials.uoc.gr>:
>>>> On 11/03/2015 09:15, Teemu Parviainen wrote:
>>>>> Hi all,
>>>>> I want to do calculations for charged oxygen vacancies in periodic
>>>>> systems (MgO surface). Does anyone have any experience what is the best
>>>>> way to do this with gpaw? I came across to a method called Virtual
>>>>> Crystal Approximation and if I understood correctly I have to change
>>>>> the
>>>>> nuclear number of all Mg atoms so that the overall change corresponds
>>>>> to
>>>>> the charge of the vacancy. Is this correct? How is this done in gpaw?
>>>>> Is
>>>>> it sufficient to just change the Z number in the PAW setup file or do I
>>>>> need to generate completely new one?
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> -Teemu Parviainen, PhD student, Jyväskylä Finland
>>>>>
>>>>> --
>>>>
>>>>
>>>> Dear all,
>>>>
>>>> I would like to ask a more general question: is it possible to use VCA
>>>> (virtual crystal approximation) in GPAW?
>>>>
>>>> This method is very efficient in alloys of atoms with similar sizes and
>>>> same
>>>> number of valence electrons, such as SiGe. Instead of using a large cell
>>>> with Si and Ge atoms, you use a small cell with virtual "SiGe" atoms.
>>>>
>>>> VCA is implemented in some codes, such as Espresso. If I understand
>>>> correctly, the pseudopotential for the virtual atom is the average of
>>>> the
>>>> two pseudopotentials. But I do not know how one could do this in GPAW.
>>>>
>>>> Any help would be appreciated. Thank you!
>>>>
>>>> best regards,
>>>> Ioannis
>>>>
>>>>
>>>> --
>>>> ----------------------------------------------
>>>> Ioannis N. Remediakis
>>>> Department of Materials Science and Technology
>>>> University Of Crete,  710 03 Heraklion, Greece
>>>> Tel: +30 2810 394250      Fax: +30 2810 394201
>>>>                  http://theory.materials.uoc.gr
>>>> ----------------------------------------------
>>>>
>>>> --
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