On 06/07/2017 13:39, Andrey Chibisov wrote:
> Dear Mohammad,
> You need to place the isolated water molecule in big cubic box (with the side
> about 15 Angstrom or bigger) and calculate the total energy. This will be the
> total energy of the isolated water molecule.
Indeed! And you can monitor the length of the box to see when the total
energy converges to the isolated limit (water has a dipole-dipole
interaction with its periodic image).
QE has also the option of using open boundary conditions, although I
admit I'm not sure where they are implemented (certainly in environ,
but maybe somewhere else).
Last, if you use periodic boundary conditions, and want to be fussy,
a bcc cell is considered the optimal traedoff - due to the fact that
for a given volume it puts the periodic neighbors quite a bit farther
(6-7%) than the cubic cell; not as much as the fcc cell, but compared
to fcc you have only 8 rather than 12 neightbours.
Probably noone in the history of simulations has tested this - so you
could make a small paper out of it!
nicola
>
> 06.07.2017, 15:30, "Ubaid Mohd" <[email protected]>:
>> Dear all,
>> I am doing the calculations of water confinement between graphene sheets. I
>> have done all the relaxation calculations. After relaxation I found the
>> total energy of the graphene sheet, I also need to find the total energy of
>> the water molecule to get the total binding energy of the system.
>> My question is, to find the total energy of the water molecule what should
>> be the crystal structure of water and how I create the unit cell of water.
>> Thanks in advance.
>>
>> Mohammad Ubaid
>> PhD Research Scholar
>> Department of Physics
>> Jamia Millia Islamia University
>> New Delhi - 110025
>>
>> On Mon, Jun 19, 2017 at 3:51 PM, Ubaid Mohd <[email protected]> wrote:
>>> Thanks Sir
>>>
>>> Mohammad Ubaid
>>> PhD Research Scholar
>>> Department of Physics
>>> Jamia Millia Islamia University
>>> New Delhi - 110025
>>>
>>> Mohammad Ubaid
>>> PhD Research Scholar
>>> Department of Physics
>>> Jamia Millia Islamia University
>>> New Delhi - 110025
>>>
>>> On Mon, Jun 19, 2017 at 3:50 PM, Giovanni Cantele
>>> <[email protected]> wrote:
>>>> Users of this forum are usually kindly requested to provide their name and
>>>> affiliation, when posting messages!!!!!!!! ;-)
>>>>
>>>> The scf run reads the position in the input file, whichever run has come
>>>> before. nscf read positions from outdir, if any
>>>>
>>>> Giovanni
>>>>
>>>>> On 19 Jun 2017, at 12:14, Ubaid Mohd <[email protected]> wrote:
>>>>>
>>>>> Then only for scf run, following the relaxation run, whether we use
>>>>> initial coordinates or optimized coordinates
>>>>>
>>>>> On Mon, Jun 19, 2017 at 3:29 PM, Giovanni Cantele
>>>>> <[email protected]> wrote:
>>>>>> Users of this forum are usually kindly requested to provide their name
>>>>>> and affiliation, when posting messages! ;-)
>>>>>>
>>>>>> If, after a relaxation run, you execute an nscf (e.g. for band structure
>>>>>> or DOS ) calculation, the code will automatically read optimised
>>>>>> positions from outdir, even though the input file contains the initial
>>>>>> coordinates. On the other hand, for an scf run, following a relaxation
>>>>>> run, even though the outdir contains information about the relaxed
>>>>>> coordinates, pw.x will always use the positions specified in the input
>>>>>> file (you might want to calculate total energy and other properties at
>>>>>> geometries other than the relaxed one).
>>>>>>
>>>>>> Giovanni
>>>>>>
>>>>>>> On 19 Jun 2017, at 09:58, Ubaid Mohd <[email protected]> wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>> I have run some relaxed calculations. In case of scf /nscf/band
>>>>>>> calculations what coordinates should I be use, optimized coordinates
>>>>>>> from relaxed output file or by default it takes from prefix
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>
> --
> Best regards,
> Andrey Chibisov. Ph.D.
> Numerical method of mathematical physics Laboratory,
> Computational Center, Russian Academy of Sciences.
> Khabarovsk, Russia
> Web page: https://www.researchgate.net/profile/A_Chibisov
> http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
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--
----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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