[Wien] accuracy problem after running x sgroup
shamik chakrabarti
shamikphy at gmail.com
Tue Oct 26 17:30:36 CEST 2010
Dear Stefan Cottenier Sir,
Thank you very much for your reply.
Yes you are right about your guess and Sir your answer really pulled us out
from lots of worries. Thank you very much Sir.
with best regards,
Shamik Chakrabarti
On Tue, Oct 26, 2010 at 5:21 PM, Stefaan Cottenier <
Stefaan.Cottenier at ugent.be> wrote:
>
> My guess might be wrong, but it looks like you call two atoms
> 'bonded/unbonded' if there is/isn't a connecting rod between them in a 3D
> display? If so, then you shouldn't worry. This is just a way of drawing
> (determined by the interatomic distance and the Z-value of the atoms
> involved). It has nothing to do with real chemical bonding. It is a display
> option that can be given as input in most (all) crystal viewers.
>
> Stefaan
>
>
>
> On 26/10/2010 11:06, shamik chakrabarti wrote:
>
>> Dear Peter Blaha Sir and wien2k users,
>>
>> We have implemented your suggestion and
>> was able to remove the space group tolerence problem. But still I have a
>> question regarding the structure. In the energy and force optimized
>> structure there are some atomic networks and atoms which are not bonded
>> with each other. The networks and atoms are remain disconnected with the
>> main atomic network. If we repeat the unit cell along x, y and z
>> direction, some networks get bonded but still there remain some free
>> networks and atoms. Thise happened as we replaced C atom in A2BCO4 by D
>> atom. Due to this replacement lattice parameter enhances but the space
>> group symmetry remains same. Hence the atoms which remain bonded in
>> A2BCO4 separated much from each other and get unbonded in A2BDO4. *Now
>> my question is this types of unbonded atomic structure is really
>> feasible although the energy and force are minimum in that
>> structure??....*
>>
>> In some experimentally generated pure phase structure also we have seen
>> such unbonded atoms and atomic network. As they are already
>> experimentally prepared they are feasible although in the unit cell some
>> atoms can be shown to be remaind unbonded. *Then how can we explain the
>> presence of the unbonded atomic networks in this experimentally prepared
>> materials??...*
>> *
>> *
>> *with best regards,*
>> *Shamik Chakrabarti
>> *
>> On Sat, Oct 23, 2010 at 12:21 PM, shamik chakrabarti
>> <shamikphy at gmail.com <mailto:shamikphy at gmail.com>> wrote:
>>
>> Dear Peter Blaha Sir,
>>
>> Thank you very much for your reply. I
>> have understand what you have said and will try to implement the
>> same. Yes it should solve the problem. Thank you sir, thank you very
>> much!!....
>>
>> with best regards,
>> Shamik Chakrabarti
>>
>>
>> On Sat, Oct 23, 2010 at 12:17 PM, Peter Blaha
>> <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.tuwien.ac.at>>
>> wrote:
>>
>> Then it simply means, that after min_lapw your atoms arrived at
>> positions, which made them nearly equivalent, so that sgroup
>> does not know within its accuracy limits if two atoms are
>> equivalent or not.
>>
>> Eventually "correct" positions manually, eg. setting atoms at
>> 0.50002 to 0.50000 and so on.
>>
>> Am 23.10.2010 08:42, schrieb shamik chakrabarti:
>>
>> Dear Peter Blaha Sir,
>> I am using wien2k_08. No it
>> is not an
>> hexagonal lattice. Actually the space group is unknown. We
>> have taken a
>> structure A2BCO4 which has space group Pnma and then
>> *replace atom C
>> with atom D *considering *primitive space group*. We have
>> used the
>> atomic coordinates and lattice constants of A2BCO4. But we
>> have made all
>> the atoms inequivalent in the new material A2BDO4 by
>> considering
>> primitive space group. It was done as we *do not want to
>> include the
>> symmetry constraints* for the atoms of this new material as
>> A2BDO4 may
>> have some different structure than A2BCO4. We want to see if
>> A2BDO4
>> structure is feasible or not and infact DFT has found a
>> structure with
>> minimum energy and minimum force on the atoms.
>>
>> with best regards,
>> Shamik Chakrabarti
>> On Sat, Oct 23, 2010 at 11:48 AM, Peter Blaha
>> <pblaha at theochem.tuwien.ac.at
>> <mailto:pblaha at theochem.tuwien.ac.at>
>> <mailto:pblaha at theochem.tuwien.ac.at
>> <mailto:pblaha at theochem.tuwien.ac.at>>> wrote:
>>
>> Are you using WIEN2k_10 ??? It should not happen anymore.
>>
>> Hexagonal lattice ??? min_lapw could have produced atomic
>> positions, which are not completely equivalent anymore
>> (like
>> 0.3333333 and 0.666666) because of rounding errors.
>>
>> Check your atomic positions manually.
>>
>> Am 23.10.2010 06:22, schrieb shamik chakrabarti:
>>
>> Dear wien2k users,
>>
>> we have done structure
>> optimization
>> (both
>> volume and force) of a A2BCO4 type material. After
>> optimization the
>> maximum force on an atom is *2.036 mRy/a.u.* After
>> optimization
>> if we
>> view the structure with xcrysden we can see that
>> some atoms remain
>> unbonded i.e. one or two free atom and the rest of
>> the structure is
>> connected through bond. Now my questions are:
>>
>> (1) Can such a structure be stable
>> although DFT has
>> able to
>> found a solution in which the energy of the unit
>> cell and forces
>> on the
>> atoms are minimum?
>>
>> (2) When I take this optimized struct
>> file and tried to
>> initilize and run a SCF with this struct file, after
>> *x sgroup*
>> command
>> it will show :
>> *Accuracy problem. Please run with different
>> tolerance (x sgroup
>> -settol
>> .00000100)*
>> *
>> *
>> Now if we ignore this problem or we
>> run the command x
>> sgroup -settol 0.00000100, irrespective of that all
>> the atoms got
>> deleted after x symmetry command!!
>>
>> So, my question is whether this
>> optimized struct
>> file is
>> not feasible or is their any way to remove this
>> accuracy problem?
>>
>> any response will be very helpful for us. Thanking you,
>>
>> with regards,
>>
>>
>> --
>> Shamik Chakrabarti
>> Research Scholar
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>>
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>> <mailto:Wien at zeus.theochem.tuwien.ac.at>>
>>
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>>
>> --
>> Peter Blaha
>> Inst.Materials Chemistry
>> TU Vienna
>> Getreidemarkt 9
>> A-1060 Vienna
>> Austria
>> +43-1-5880115671
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>> Wien mailing list
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>>
>>
>>
>> --
>> Shamik Chakrabarti
>> Research Scholar
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>>
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>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
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>>
>>
>> --
>> Peter Blaha
>> Inst.Materials Chemistry
>> TU Vienna
>> Getreidemarkt 9
>> A-1060 Vienna
>> Austria
>> +43-1-5880115671
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> <mailto:Wien at zeus.theochem.tuwien.ac.at>
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>>
>>
>>
>> --
>> Shamik Chakrabarti
>> Research Scholar
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>>
>>
>> --
>> Shamik Chakrabarti
>> Research Scholar
>> Dept. of Physics & Meteorology
>> Material Processing & Solid State Ionics Lab
>> IIT Kharagpur
>> Kharagpur 721302
>> INDIA
>>
>>
>>
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>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>
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>
--
Shamik Chakrabarti
Research Scholar
Dept. of Physics & Meteorology
Material Processing & Solid State Ionics Lab
IIT Kharagpur
Kharagpur 721302
INDIA
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