[Pw_forum] Quantum Espresso
Biswajit Santra
bishalya at gmail.com
Thu Jul 6 20:23:20 CEST 2017
You can find many water crystal structure here
http://aip.scitation.org/doi/suppl/10.1063/1.4824481
However, you may not need it since you need isolated water molecule energy.
A large cell of about 20-25 Angstrom length is typically sufficient to have
negligible interactions with the periodic images.
Best,
Biswajit Santra
Mobile: +1-609-227-9202
http://www.princeton.edu/~bsantra/
On Thu, Jul 6, 2017 at 12:07 PM, Ubaid Mohd <onlymubaid at gmail.com> wrote:
> Should I relax the isolated water molecule inside the cubical box?
>
> On 6 Jul 2017 5:17 pm, "Nicola Marzari" <nicola.marzari at epfl.ch> wrote:
>
>> 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" <onlymubaid at gmail.com>:
>> >> 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 <onlymubaid at gmail.com>
>> 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 <
>> giovanni.cantele at spin.cnr.it> 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 <onlymubaid at gmail.com> 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 <
>> giovanni.cantele at spin.cnr.it> 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 <onlymubaid at gmail.com>
>> 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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>> >> ,
>> >>
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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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