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 <onlymub...@gmail.com> wrote: > Should I relax the isolated water molecule inside the cubical box? > > On 6 Jul 2017 5:17 pm, "Nicola Marzari" <nicola.marz...@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" <onlymub...@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 <onlymub...@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.cant...@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 <onlymub...@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.cant...@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 <onlymub...@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 >> >>>>>>> _______________________________________________ >> >>>>>>> Pw_forum mailing list >> >>>>>>> Pw_forum@pwscf.org >> >>>>>>> http://pwscf.org/mailman/listinfo/pw_forum >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> Pw_forum mailing list >> >>>>>> Pw_forum@pwscf.org >> >>>>>> http://pwscf.org/mailman/listinfo/pw_forum >> >>>>> _______________________________________________ >> >>>>> Pw_forum mailing list >> >>>>> Pw_forum@pwscf.org >> >>>>> http://pwscf.org/mailman/listinfo/pw_forum >> >>>> >> >>>> _______________________________________________ >> >>>> Pw_forum mailing list >> >>>> Pw_forum@pwscf.org >> >>>> http://pwscf.org/mailman/listinfo/pw_forum >> >> , >> >> >> >> _______________________________________________ >> >> Pw_forum mailing list >> >> Pw_forum@pwscf.org >> >> 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 >> > Pw_forum@pwscf.org >> > 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 >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum >
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