[QE-users] How H2O molecule reflect DFT scf calculation at 0 Kelvin calculation
Stefano de Gironcoli
degironc at sissa.it
Sun Aug 28 13:46:59 CEST 2022
CP dynamics requires the existence of a gap in the electronic spectrum.
you can force cp.x to minimize the electronic state by using "cg" as
electron_dynamics method. I would use pw.x to perform BOMD but if you
are more familiar with cp.x you can try that.
stefano
On 27/08/22 15:47, Jayraj Anadani wrote:
> 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
>>> > 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 <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 <http://www.max-centre.eu>)
>>> users mailing listusers 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
>> <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 <http://www.max-centre.eu>)
>> users mailing listusers 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
> <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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20220828/f5aedb32/attachment.html>
More information about the users
mailing list