Should I relax the isolated water molecule inside the cubical box? On 6 Jul 2017 5:17 pm, "Nicola Marzari" <[email protected]> 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" <[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 > >>>>>>> _______________________________________________ > >>>>>>> Pw_forum mailing list > >>>>>>> [email protected] > >>>>>>> http://pwscf.org/mailman/listinfo/pw_forum > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Pw_forum mailing list > >>>>>> [email protected] > >>>>>> http://pwscf.org/mailman/listinfo/pw_forum > >>>>> _______________________________________________ > >>>>> Pw_forum mailing list > >>>>> [email protected] > >>>>> http://pwscf.org/mailman/listinfo/pw_forum > >>>> > >>>> _______________________________________________ > >>>> Pw_forum mailing list > >>>> [email protected] > >>>> http://pwscf.org/mailman/listinfo/pw_forum > >> , > >> > >> _______________________________________________ > >> Pw_forum mailing list > >> [email protected] > >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > > -- > > 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 > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > ---------------------------------------------------------------------- > 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 > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum >
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