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

Fri Aug 26 15:01:00 CEST 2022

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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>
> _______________________________________________
> 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
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