[Pw_forum] Quantum Espresso

Thu Jul 6 18:07:52 CEST 2017

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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