<div dir="auto">Should I relax the isolated water molecule inside the cubical box?</div><div class="gmail_extra"><br><div class="gmail_quote">On 6 Jul 2017 5:17 pm, "Nicola Marzari" <<a href="mailto:nicola.marzari@epfl.ch">nicola.marzari@epfl.ch</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 06/07/2017 13:39, Andrey Chibisov wrote:<br>
> Dear Mohammad,<br>
> 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.<br>
<br>
Indeed! And you can monitor the length of the box to see when the total<br>
energy converges to the isolated limit (water has a dipole-dipole<br>
interaction with its periodic image).<br>
<br>
QE has also the option of using open boundary conditions, although I<br>
admit I'm not sure where they are implemented (certainly in environ,<br>
but maybe somewhere else).<br>
<br>
Last, if you use periodic boundary conditions, and want to be fussy,<br>
a bcc cell is considered the optimal traedoff - due to the fact that<br>
for a given volume it puts the periodic neighbors quite a bit farther<br>
(6-7%) than the cubic cell; not as much as the fcc cell, but compared<br>
to fcc you have only 8 rather than 12 neightbours.<br>
<br>
Probably noone in the history of simulations has tested this - so you<br>
could make a small paper out of it!<br>
<br>
nicola<br>
<br>
<br>
><br>
> 06.07.2017, 15:30, "Ubaid Mohd" <<a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a>>:<br>
>> Dear all,<br>
>> 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.<br>
>> 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.<br>
>> Thanks in advance.<br>
>><br>
>> Mohammad Ubaid<br>
>> PhD Research Scholar<br>
>> Department of Physics<br>
>> Jamia Millia Islamia University<br>
>> New Delhi - 110025<br>
>><br>
>> On Mon, Jun 19, 2017 at 3:51 PM, Ubaid Mohd <<a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a>> wrote:<br>
>>> Thanks Sir<br>
>>><br>
>>> Mohammad Ubaid<br>
>>> PhD Research Scholar<br>
>>> Department of Physics<br>
>>> Jamia Millia Islamia University<br>
>>> New Delhi - 110025<br>
>>><br>
>>> Mohammad Ubaid<br>
>>> PhD Research Scholar<br>
>>> Department of Physics<br>
>>> Jamia Millia Islamia University<br>
>>> New Delhi - 110025<br>
>>><br>
>>> On Mon, Jun 19, 2017 at 3:50 PM, Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a>> wrote:<br>
>>>> Users of this forum are usually kindly requested to provide their name and affiliation, when posting messages!!!!!!!! ;-)<br>
>>>><br>
>>>> The scf run reads the position in the input file, whichever run has come before. nscf read positions from outdir, if any<br>
>>>><br>
>>>> Giovanni<br>
>>>><br>
>>>>> On 19 Jun 2017, at 12:14, Ubaid Mohd <<a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a>> wrote:<br>
>>>>><br>
>>>>> Then only for scf run, following the relaxation run, whether we use initial coordinates or optimized coordinates<br>
>>>>><br>
>>>>> On Mon, Jun 19, 2017 at 3:29 PM, Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a>> wrote:<br>
>>>>>> Users of this forum are usually kindly requested to provide their name and affiliation, when posting messages! ;-)<br>
>>>>>><br>
>>>>>> 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).<br>
>>>>>><br>
>>>>>> Giovanni<br>
>>>>>><br>
>>>>>>> On 19 Jun 2017, at 09:58, Ubaid Mohd <<a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a>> wrote:<br>
>>>>>>><br>
>>>>>>> Dear all,<br>
>>>>>>> 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<br>
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>> ,<br>
>><br>
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><br>
><br>
> --<br>
> Best regards,<br>
> Andrey Chibisov. Ph.D.<br>
> Numerical method of mathematical physics Laboratory,<br>
> Computational Center, Russian Academy of Sciences.<br>
> Khabarovsk, Russia<br>
> Web page: <a href="https://www.researchgate.net/profile/A_Chibisov" rel="noreferrer" target="_blank">https://www.researchgate.net/<wbr>profile/A_Chibisov</a><br>
> <a href="http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en" rel="noreferrer" target="_blank">http://ru.linkedin.com/pub/<wbr>andrey-chibisov/55/253/986/en</a><br>
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<br>
<br>
--<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL<br>
Director, National Centre for Competence in Research NCCR MARVEL, EPFL<br>
<a href="http://theossrv1.epfl.ch/Main/Contact" rel="noreferrer" target="_blank">http://theossrv1.epfl.ch/Main/<wbr>Contact</a> <a href="http://nccr-marvel.ch/en/project" rel="noreferrer" target="_blank">http://nccr-marvel.ch/en/<wbr>project</a><br>
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