[Wien] accuracy problem after running x sgroup
Stefaan Cottenier
Stefaan.Cottenier at UGent.be
Tue Oct 26 13:51:37 CEST 2010
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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>
> --
> Peter Blaha
> Inst.Materials Chemistry
> TU Vienna
> Getreidemarkt 9
> A-1060 Vienna
> Austria
> +43-1-5880115671
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> <mailto:Wien at zeus.theochem.tuwien.ac.at
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>
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>
>
>
>
> --
> Shamik Chakrabarti
> Research Scholar
> Dept. of Physics & Meteorology
> Material Processing & Solid State Ionics Lab
> IIT Kharagpur
> Kharagpur 721302
> INDIA
>
>
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> <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
> _______________________________________________
> 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
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