[Wien] Your spheres are unphsically small Error

Wed Dec 11 19:37:01 CET 2019

Internal optimization will handle this; I suggest doing this first to get
an adequate starting point (then do volume+internal).

I STRONGLY suggest that you check the bond-valence sums (BVS) first as this
is trivial. The H should be near 1, the O near 2 etc (within standard
deviations, e.g. google BVS.)

On Wed, Dec 11, 2019 at 12:29 PM Ashwani Kumar <ashwani.ism at gmail.com>
wrote:

> I was thinking the same : changed H atom (36th) x,y,z coordinates very
> minutely to make O-H bond : ~1.6 bohr (equiavalent to other O-H bonds in
> crystal structure). Now x_nn did executed without any error or warning. Is
> there any code/programe available where if bond length between two atoms is
> increased then it can give new exact x,y,z coordinates. Becoz it's
> difficult to select manually x,y,z coordinates which just increase the bond
> length but do not disturb bond angles/dihedral arrangements.
>
> thanking you,
> A. Kumar
>
> On Wed, Dec 11, 2019 at 9:14 AM Laurence Marks <laurence.marks at gmail.com>
> wrote:
>
>> Move the H away from the O until:
>> a) The BVS is reasonable
>> b) The OH bond distance is standard.
>>
>> This requires some thought.
>>
>> _____
>> Professor Laurence Marks
>> "Research is to see what everybody else has seen, and to think what
>> nobody else has thought", Albert Szent-Gyorgi
>> www.numis.northwestern.edu
>>
>> On Tue, Dec 10, 2019, 20:39 Ashwani Kumar <ashwani.ism at gmail.com> wrote:
>>
>>> Hi,
>>>     As Dr. Marks pointed out earlier in thread:
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19343.html
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg19343.html&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=tmxUIGqkGPUE2B9vKa94qPzZlRrSqFalVBVkac_d0-g&s=mJZnNEHW7hDpV9184I4a_Vzz5qnHCvwoXr_mP75GnJY&e=>
>>> &
>>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19331.html
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg19331.html&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=tmxUIGqkGPUE2B9vKa94qPzZlRrSqFalVBVkac_d0-g&s=O5bY_OIAuMM_tXOEcd9xxn_GnQSBVs6-ozOzSmMcVqo&e=>
>>> about missing of Hydrog in struct file of KHfOxalate (formula :
>>> K4Hf(C2O4)4.5H2O). Could not found any other struc. data which mentions
>>> coordinates of Hydrogen. However, structural file of K4Zr(C2O4)4.5H2O (ICSD
>>> database) contains the Hydrogen position coordinates. Plan is to remove Zr
>>> by Hf keeping rest same. But x_nn giving error during init_lapw.
>>> "Your spheres are unphysically small. Most likely your str is wrong and
>>> will lead to a crash later"  when default rmt accepted (even with reduction
>>> 0%). when i fixed RMT of Oxygen : 0.9 and Hydro:0.5 then case.outputnn
>>> shows error for "atom 22 and 36 : Sums to 1.3700 GT *NNN*-Dis=1.3584"
>>>
>>> *Summary :: init_lapw program not accepting RMT of Hydr. below 0.5 and
>>> oxygen below 0.9 But when given H:0.5 and O:0.9, case.outputnn shows error *
>>> case_setrmt.struct filei s attached (next post).
>>> How to get rid of this error.
>>>
>>> thanks,
>>> A. kumar
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
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>>>
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-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
Corrosion in 4D: www.numis.northwestern.edu/MURI
Co-Editor, Acta Cryst A
"Research is to see what everybody else has seen, and to think what nobody
else has thought"
Albert Szent-Gyorgi
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