The ABINIT Users Mailing List ( CLOSED )

[ren <opticalcase@gmail.com>]

Hi Dr Kondor:

Thank you for your advice! May I ask you further, because i need to
consider supercell in the future, so nomally, i build the supercell
say 3x3x3 using Materials Studio GUI which I use Cell2Abinit.py script
to convert the structure into Abinit input data. What Materials Studio
does is that to build a supercell, it will convert into a P1 symmetry
structure, its a primitive structure I suppose? If that's the case,
will optcell=2 recognize it as a P1 symmetry or its original P63mc
symmetry? If it is a P1symmetry, will it still contraint a=b?

If using P1 symmetry does not constraint e.g a = b, then either i have
to use the step by step method I use (optcell=1) to do the geometry
optimization or i have to rebuild my input file that has the supercell
but with its original symmetry (can it be done in this way?)

 I seems to get confuse when to use a primitive cell or not, do I?

I have not tried to see the difference and still a beginner in the
simulation field. I am anticipating such problem might occur.

My email seems incoherent. My apology.

Cheers,
Yee Yan

On Wed, Mar 25, 2009 at 9:55 PM, Jess Kondor <kondor.jess@gmail.com> wrote:
> Dear Yee Yan,
>
>  My understanding is the following - if abinit found a space group of
> the material, it will conserve the symmetry (until otherwise
> requested) during cell relaxation. In other words, 'a' would be always
> equal 'b' for your case.
>
> jess.
>
> On Wed, Mar 25, 2009 at 7:01 AM, ren <opticalcase@gmail.com> wrote:
>> Hi Dr Kondor:
>>
>> I have not tried optcell 2 yet. Because of the symmetry problem in my
>> materials where a=b must be constrained, i tried to search the forum
>> to see if anyone would verify optcell=2 could do this but seem none
>> talk about it. So i have a little doubt and decide to try other method
>> first before hitting on this option. My bad.. my apology.
>>
>> Cheers,
>> Yee Yan
>>
>> On Tue, Mar 24, 2009 at 7:49 PM, Jess Kondor <kondor.jess@gmail.com> wrote:
>>> Hello,
>>>
>>>  May be I wrong, but why you don't use an automatic cell optimization
>>> (optcell=2) combined with ionic relaxation (ionmov=2) for your
>>> purpose?
>>>
>>> jess
>>>
>>>
>>> On Mon, Mar 23, 2009 at 2:01 PM, ren <opticalcase@gmail.com> wrote:
>>>> Dear Prof Zwanziger, Dr Matthieu and Dr Dong:
>>>>
>>>> Thank you for your valuable advices! My apology for the late reply.
>>>>
>>>> I did some preliminary work on increasing the Ecut and no of kpts, the
>>>> results seems to be better.
>>>>
>>>> I will work on using optcell=2 as well as strtarget to see how's the 
>>>> result.
>>>>
>>>> Thanks once again!
>>>>
>>>> Cheers
>>>> Yee Yan
>>>>
>>>>
>>>> On Sun, Mar 22, 2009 at 2:52 AM, St Druid <tq02ksu@gmail.com> wrote:
>>>>> Hello users:
>>>>>
>>>>> Invariance of lattice parameter a and b is determined by the symmetry,
>>>>> unless you set the "nsym = 1 ",  according to the origin of the E-V
>>>>> curve, I would like to suggest that, setting optcell = 2, and serial
>>>>> strtarget values to obtain deferent volumes, than plot it.
>>>>>
>>>>> Regards.
>>>>>
>>>>> On Sat, Mar 21, 2009 at 10:14 AM, ren <opticalcase@gmail.com> wrote:
>>>>>> Dear All:
>>>>>>
>>>>>> I am doing geometry optimization for ZnO which has a hexagonal
>>>>>> geometry. The lattice a and b is equal. Therefore, a and b should
>>>>>> change by the same amount. Since it has a space group of P63 mc,
>>>>>> therefore, only the oxygen atoms is able to vary in its z (or u i
>>>>>> suppose) direction , internal coordinate.
>>>>>>
>>>>>> I read up the optimization notes  by L. D. Marks, which is meant for
>>>>>> Wien2k, but i guess it should be applicable universally. What is done
>>>>>> is that, having 5 different volumes having the same a:b:c ratio, the
>>>>>> internal coordinates are optimized. Thereafter, for 5 c/a ratio, each
>>>>>> with 5 different volume, the internal coordinate are optimized.
>>>>>>
>>>>>> At the moment, I tried the first step. But I tried exploring a larger
>>>>>> range of volumes (26 different volumes). By plotting the volumes vs
>>>>>> total energy, it appears that there is 2 local minimal (See the
>>>>>> picture attached. I supposed one would choose the minimal with the
>>>>>> lowest energy ? The volume obtained for the lowest energy is
>>>>>> 313.992080 bohr^3. The other local minimal with a higher energy has a
>>>>>> volume of 294.765030 bohr^3
>>>>>>
>>>>>> The problem occurs when I tried to use optcell=1 to see one could get
>>>>>> similar result. It appears that the result obtained has a optimized
>>>>>> volume similar to 294.765030 bohr^3 which has an energy similar to the
>>>>>> local minimal that has a higher energy as obtained from my first
>>>>>> study. I have also attached the email with both input files together.
>>>>>>
>>>>>> For optcell=1, here is the options i used
>>>>>>
>>>>>> optcell 1 # with optimization of volume only, do not modify rprim and
>>>>>> allow an homogeneous dilation of the 3 component of acell
>>>>>> ionmov 2 # Broyden Steps
>>>>>> ntime 40
>>>>>> dilatmx 1.05
>>>>>> ecutsm 0.5
>>>>>> tolmxf 5.0d-5
>>>>>> toldff 5.0d-6
>>>>>>
>>>>>> I am using Troullier-Martins psp.
>>>>>>
>>>>>> I tried to increase ntime, tolmxf to 5.0d-7 and toldff to 5.0d-7 but
>>>>>> the same results are obtained.
>>>>>>
>>>>>> May I know if anyone can advised me what i have missed out that caused
>>>>>> this discrepancy?
>>>>>> Should using optcell=1 be more accurate than manually optimized the
>>>>>> internal coordinate with different volumes with fixed a:b :c ratio?
>>>>>>
>>>>>> Lastly, i read from the mailing list and it is always recommended to
>>>>>> use optcell=2? Because of this spacegroup, does anyone have experience
>>>>>> that optcell=2 ensure that lattice a=b always expand and contract by
>>>>>> the same amount and that only the z internal coordinate is optimized?
>>>>>>
>>>>>> Hope like to hear from your advices!!
>>>>>>
>>>>>> Sorry for the lengthy email.
>>>>>>
>>>>>> Cheers,
>>>>>> Yee Yan
>>>>>> School of Materials Science and Engineering
>>>>>> Nanyang Technological University (Singapore)
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> B.W Dong
>>>>> State Key Laboratory of Superhard Material
>>>>> jilin university, Changchun Jilin, China. 130012
>>>>>
>>>>> tq02ksu@gmail.com [ tq02ksu@email.jlu.edu.cn ]
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> =====================================
>>> Jess Kondor
>>>
>>> NSTI
>>> =====================================
>>>
>>>
>>
>>
>
>
>
>
> --
> =====================================
> Jess Kondor
>
> NSTI
> =====================================
>
>