[Wien] a doubt from threads in case.InM
fatima DFT
fatimadft5 at gmail.com
Fri Aug 4 09:25:52 CEST 2017
So, it does not effect the results if one uses all zeros in respective row
or zero at first three places (x, y, z) and 1.0 at the last place. Correct?
On Fri, Aug 4, 2017 at 12:52 PM, Peter Blaha <pblaha at theochem.tuwien.ac.at>
wrote:
> It is NOT a divisor ! (does not make sense here). Depending on the method
> the 4th value is not used or is eg. a friction term for damped newton
> dynamics.
>
> On 08/04/2017 02:26 AM, Gavin Abo wrote:
>
>> Currently too lazy to check, are the data values x y z div (where div is
>> the divisor)?
>>
>> So (x y z)/div:
>>
>> 0.0. 0.0 0.0 0.0 => (0, 0, 0)/0 = undefined [1] <- If it is not giving a
>> divide by zero error [2], it sounds like the code is able to handle it
>> and may be setting any of these divisions to 0.
>>
>> 0.0. 0.0 0.0 1.0 => (0, 0, 0)/1 = (0, 0, 0) <- This may be safer to use.
>>
>> [1] https://en.wikipedia.org/wiki/Division_by_zero
>>
>> [2]
>> https://software.intel.com/en-us/forums/intel-fortran-compil
>> er-for-linux-and-mac-os-x/topic/392791
>>
>> On 8/3/2017 9:26 AM, fatima DFT wrote:
>>
>>> Thank you very much Sir.
>>> I feel relax now.
>>> I did a heavy calculation using 0.0. 0.0 0.0 0.0 instead of 0.0. 0.0
>>> 0.0 1.0
>>>
>>> So I was worried to repeat the calculation by fixing the position with
>>> 0.0. 0.0 0.0 1.0.
>>>
>>> On Thu, Aug 3, 2017 at 8:31 PM, Laurence Marks
>>> <L-marks at northwestern.edu <mailto:L-marks at northwestern.edu>> wrote:
>>>
>>> Inlined
>>>
>>> On Thu, Aug 3, 2017 at 9:49 AM, fatima DFT <fatimadft5 at gmail.com
>>> <mailto:fatimadft5 at gmail.com>> wrote:
>>>
>>> Dear Prof. Peter, Oleg and Marks,
>>>
>>> I have two queries for case.inM
>>>
>>> First:
>>>
>>> I stuck on case.inM file where I want to fix the positions of
>>> the heavier atom for which I do not want to relax the structure.
>>>
>>>
>>> A comment: fixing atoms does not do what people think, in general
>>> it does not make the convergence of QM methods faster (it can for
>>> CG). The convergence depends upon the number and density of the
>>> elastic eigenvectors (PORT) and the elastic-electronic system
>>> (MSR1a).
>>>
>>>
>>> In one thread Prof Peter
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
>>> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
>>> msg03285.html&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_
>>> d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=
>>> lMntW40NGNoDrUMHYVU-vXvlVw2pGHikT4XpBt9gMhU&s=-6101yYtzjIzQW
>>> csyC0Zc5AQTUAs08Rf0kz5Ifefu7I&e=>
>>> mentioned keeping 0 0 0 0 in the respective row of atom that I
>>> want to constrain. But this four zeros means the entire line
>>> should be zero
>>>
>>> 0.0 0.0 0.0 0.0 #Atom 1 Generated by pairhess >>> Say
>>> it is for La atom.
>>>
>>> As per Prof Marks
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
>>> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
>>> msg12403.html&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_
>>> d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=
>>> lMntW40NGNoDrUMHYVU-vXvlVw2pGHikT4XpBt9gMhU&s=0fcEvAFHmpT7Za
>>> hxBQYrqD0Xr0DEsgKPFE0Nk-fLeLM&e=>and
>>> Prof. Oleg
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.
>>> mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_
>>> msg01858.html&d=DwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_
>>> d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=
>>> lMntW40NGNoDrUMHYVU-vXvlVw2pGHikT4XpBt9gMhU&s=GJxC2Mi9-
>>> Fts6rULojSPz0X_acMQL2Oe5Ie7WXILcr0&e=>
>>>
>>> The only first three number should be zero
>>>
>>> 0.0 0.0 0.0 1.0 #Atom 1 Generated by pairhess
>>>
>>> Could you please clear my doubt that:
>>>
>>> How the results will differ if I will use "0.0 0.0 0.0 0.0
>>> #Atom 1 Generated by pairhess" instead of 0.0 0.0 0.0 1.0 ?
>>>
>>>
>>> I am 99% confident that they are equivalent.
>>>
>>>
>>> Second:
>>>
>>> If I use "x pairhess" to generate the case.inM then does it
>>> copy the case.inM according to the structure files? I just
>>> tested it for two different structures and I saw two different
>>> kind of case.inM.
>>>
>>>
>>> Yes, different structures with different symmetries have different
>>> symmetry constrained sites so different case.inM.
>>>
>>>
>>>
>>> Thank you in advance
>>>
>>> regards
>>> Fatima
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>> <http://www.numis.northwestern.edu> ; Corrosion in 4D:
>>> MURI4D.numis.northwestern.edu <http://MURI4D.numis.northwestern.edu>
>>> Partner of the CFW 100% program for gender
>>> equity, www.cfw.org/100-percent <http://www.cfw.org/100-percent>
>>> Co-Editor, Acta Cryst A
>>>
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>>
>>
>>
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>>
> --
>
> P.Blaha
> --------------------------------------------------------------------------
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: blaha at theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at
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