[QE-users] How H2O molecule reflect DFT scf calculation at 0 Kelvin calculation

Fri Aug 26 18:34:00 CEST 2022

I appreciate your help
Thank you very much sir.

On Fri, 26 Aug, 2022, 7:16 pm Stefano de Gironcoli, <degironc at sissa.it>
wrote:

> I would take out small clusters from your 10000 cells (possibly saturate
> with H atoms if you cut covalent bonds), not relax (with the exception of
> relaxing the extra H atoms you added to saturate), compute atomic PDOS of
> the central atom(s) and verify that for increasing number of atoms in the
> clusters these quantities stabilize and converge.
>
> if a significant size dependence results you may want to play with the
> environ feature (http://www.quantum-environ.org/)  to minimize boundary
> effects
>
> stefano
> On 26/08/22 15:01, Jayraj Anadani wrote:
>
> I have one amorphorse metallic system of 10000 atoms in which several
> clusters are in it. I want to calculate atomic bonding and electronic
> interaction through finding DOS/PDOS and Charge analysis of a small cluster
> part of a large amorphorse metallic system.
> My cluster size is upto 13 to 25 atoms which is part of large md
> simulation.
>
> So can i have to do relaxation or i can directly do scf calculation with
> restricted parameter ?
>
> Thank you
>
> On Fri, 26 Aug, 2022, 6:04 pm Stefano de Gironcoli, <degironc at sissa.it>
> wrote:
>
>> I dont think that a 10-20 atom cluster configuration extracted from a
>> 10000 condensed phase has anything to do with the same system at 300 K.
>>
>> possibly some electronic properties of the central molecule may be
>> similar to the corresponding properties in the condensed phase but no
>> guarantee.
>>
>> if you relax or perform md for the cluster you loose your (tiny)
>> connection with the original cell.
>> I fail to understand what is your problem and what you would like to
>> compute/understand
>>
>> stefano
>>
>> On 26/08/22 13:52, Jayraj Anadani wrote:
>>
>> Thank you sir, for your reply
>> but I have one particular molecular system of 10-20 atoms which I am
>> getting from a simulation of a large atom (around 10000 atoms) at a 300K
>> temperature from a molecular dynamic simulation (LAMMPS). and I also did
>> optimization of that MD structure which is amorphous metallic glass. Now,
>>  Can I do dft study of a small part of a single molecule of a large MD
>> simulation(~10000 atoms) ?
>> till now i did below things but i am bit confused which way is best way
>> to study DFT . i also dis AIMD/CPMD but for metallic glass CPMD doesn't
>> work good with PAW PP.
>> so,
>> 1. Can I do direct SCF calculation(without relax) by giving a condition
>> of *forc_conv_thr* and *tot_conv_thr* with creating a vacuum(for a
>> non-periodic system) of around 15 Angstrom to converge properly. *OR*
>> 2. I should do the RELAX calculation with vacuum and then go to the *scf* calculation
>> to find the total energy and then *nscf*.
>>
>> ***questions:
>> 1. what if I relax a system and position is changed a bit(which is
>> obvious) to minimize the total energy but that energy is at zero kelvin dft
>> calculation and I want to study the system at 300K. So how can small parts
>> of a structure reflect large MD simulation structural properties?
>> Thank you
>> regards
>> jayraj anadani
>> Ph.D. Research scholar Department of physics
>> sardar patel university
>> india
>>
>> On Fri, Aug 26, 2022 at 5:00 PM Stefano de Gironcoli <degironc at sissa.it>
>> wrote:
>>
>>> Dear JAYRAJ ANADANI,
>>>
>>>   calculation="scf"  corresponds to a minimization of the total energy
>>> at fixed atomic positions. you chose where to put the ions. the code
>>> does its best to return the corresponding energy.
>>>
>>>   calculaiton="relax" corresponds to a series of scf calculations,
>>> followed by forces evaluation and geometry update to minimize the energy
>>> of the system. The code does its best to converge to a minimum (non
>>> necessarily the global minimum) in the GS potential energy surface.
>>>
>>>   there is no temperature in any of these calculations.
>>>
>>>   if you want to simulate the system at finite (classical) temperature
>>> for the atoms you should perform MD simlations
>>>
>>> stefano
>>>
>>> On 26/08/22 05:02, Jayraj Anadani wrote:
>>> > Dear QE
>>> >               I put H2O molecular atoms small far apart from each
>>> > other within large supercell so that the periodic image of the H2O do
>>> > not interact with each other and run a scf calculation my convergence
>>> > done successfully with good amount of accuracy upto 10^-9. But it is
>>> > not reflecting original H2O molecule at 300 Kelvin...but when i
>>> > relaxing these atoms and then did scf calculation they are reflecting
>>> > H2O at 300k by observing bond angel and length.. how ? And my question
>>> is
>>> > 1) scf is also doing calculation using iteration method algorithm by
>>> > using electronic densities at ground state so why they converge when
>>> > two hydrogen atoms and one oxygen atom are not at appropriate
>>> > distance.still scf converge how ?
>>> > 2) also by doing relax calculation all of sudden two hydrogen and one
>>> > oxygen come closer and they formed a bond and bond angel which is
>>> > reflect 300k H2O molecule structure. So how two hydrogen and one
>>> > oxygen atoms knows during relaxation that i have to make structure at
>>> > a room temperature?
>>> >
>>> >
>>> > Thank you
>>> > Regards
>>> >
>>> > JAYRAJ ANADANI
>>> > Ph.D Research scholar
>>> > Department of physics
>>> > Sardar Patel University
>>> > Anand,Gujarat,
>>> > India
>>> >
>>> > _______________________________________________
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>>> effects that the Russian military offensive has on their
>>> country and on the free and peaceful scientific, cultural,
>>> and economic cooperation amongst peoples
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>>
>>
>> _______________________________________________
>> The Quantum ESPRESSO community stands by the Ukrainian
>> people and expresses its concerns about the devastating
>> effects that the Russian military offensive has on their
>> country and on the free and peaceful scientific, cultural,
>> and economic cooperation amongst peoples
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>
>> _______________________________________________
>> The Quantum ESPRESSO community stands by the Ukrainian
>> people and expresses its concerns about the devastating
>> effects that the Russian military offensive has on their
>> country and on the free and peaceful scientific, cultural,
>> and economic cooperation amongst peoples
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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