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

Sat Aug 27 15:47:25 CEST 2022

Hello sir,
I have one more question regarding this : can I perform the cpmd simulation
method using cp.x in quantum espresso to simulate the metallic glass system
? I did this cpmd but I couldn't control the kinetic energy of the
electrons because my system is amorphorse metallic and according to CP user
guide the cpmd is not performing well with amorphous metallic systems. or
is BOMD using pwscf by doing the reduce-T option is good for studying
metallic glass ?

kindly suggest a feasible method to do DFT study of metallic glass alloys
using quantum espresso package.

thank you

regards
jayraj anadani

On Fri, Aug 26, 2022 at 10:04 PM Jayraj Anadani <jayrajanadani at spuvvn.edu>
wrote:

> 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
>>>> >
>>>> > _______________________________________________
>>>> > The Quantum ESPRESSO community stands by the Ukrainian
>>>> > people and expresses its concerns about the devastating
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>>>> > country and on the free and peaceful scientific, cultural,
>>>> > and economic cooperation amongst peoples
>>>> > _______________________________________________
>>>> > Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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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.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
>>
>>
>> _______________________________________________
>> 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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