[QE-users] How H2O molecule reflect DFT scf calculation at 0 Kelvin calculation
Stefano de Gironcoli
degironc at sissa.it
Fri Aug 26 15:46:03 CEST 2022
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 <http://www.max-centre.eu>)
>> users mailing listusers at lists.quantum-espresso.org
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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
> <http://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 listusers at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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