[QE-users] Binding energy and interatomic force constant

[KRISHNENDU MUKHERJEE]

Dear all, 

Thank you for continuing the discussion. Please allow me to write why I asked 
the question. I am trying to find out a methodology to find the effect of 
grain-size on binding energy. I think one way is to compare the total-energy of 
the system from pwscf calculation for different grain-sizes. But then I think 
the total-energy will also include the surface energy. So, now I put my 
question in a different way. Is there a way to find out the binding energy from 
the total-energy ? 

Thank you, 
Regards, 
Krishnendu 

--
 

Dear Prof. Baroni, 

Hi. 
Thank you so much for your detailed clarification. 

Best regards, 
Mahmoud Payami 
- Original Message - 
From: Stefano Baroni (BARONI at sissa.it) 
Date: 07/01/1403 21:53 
To: Mpayami (mpayami at aeoi.org.ir), Quantum ESPRESSO users Forum (users at 
lists.quantum-espresso.org) 
Subject: Re: [QE-users] Binding energy and interatomic force constant 

Here, I beg to differ. The binding is defined as the energy necessary to bring 
all the atoms from their equilibrium position (Δx=0) to an infinite distance 
from each other (Δx=\infty). In any harmonic model, evidently, this energy 
would be infinite. The problem is, the harmonic model, within which interatomic 
force constants are defined, is only meaningful in the neighbourhood of the 
equilibrium position and does not say anything about the forces acting on atoms 
far from it. Hope this clarifies a bit. Stefano B 


On 26 Mar 2024, at 18:51, Mpayami via users  wrote: 


Dear Krishnendu, 

Hi. 
I add a few words to Prof. Stefano Baroni's reply: 
Suppose you have a harmonic spring obeying Hook's law, for which the stored 
energy is E=K*(Δx)^2/2. 
Here, K plays the role of interatomic force constant. As you see, just knowing 
K one can not calculate 
the stored energy unless on knows the value of Δx. 

Bests 

--- 
Mahmoud Payami 
NSTRI, AEOI,Tehran, Iran 
Email: mpayami at aeoi.org.ir 
Phone: +98(0)2182066504 
 

- Original Message - 
From: Stefano Baroni (baroni at sissa.it) 
Date: 06/01/1403 11:41 
To: Quantum ESPRESSO users Forum (users at lists.quantum-espresso.org) 
Subject: Re: [QE-users] Binding energy and interatomic force constant 

No. SB 

___ 
Stefano Baroni, Trieste --http://stefano.baroni.me 

On 25 Mar 2024, at 07:15, KRISHNENDU MUKHERJEE  
wrote: 




Dear all, 


Can I compute the binding energy of a nano-crystal from the interatomic force 
constant ? 


Thanking you, 
Best regards, 
Krishnendu 




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[QE-users] Binding energy and interatomic force constant

[KRISHNENDU MUKHERJEE]

Dear all, 

Can I compute the binding energy of a nano-crystal from the interatomic force 
constant ? 

Thanking you, 
Best regards, 
Krishnendu 

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[QE-users] Example 8 of CPV

[KRISHNENDU MUKHERJEE]

Hello, 

When I did the example 8 of CPV I got some additional outputs as compared to 
the reference output. 

* Physical Quantities at step: 10 
Total Electronic Pressure (GPa) -25.47840 10 
Total Electronic Pressure (GPa) -36.11474 10 
 
… 
Total Electronic Pressure (GPa) -80.93476 10 
Total Electronic Pressure (GPa) -80.13102 10 
Total Electronic Pressure (GPa) -9.21239 10 
Total Electronic Pressure (GPa) -79.82307 10 
Total Electronic Pressure (GPa) -80.00089 10 
Total Electronic Pressure (GPa) -79.87797 10 
…… 
….. 
Total Electronic Pressure (GPa) -1.42098 10 
Total Electronic Pressure (GPa) -1.42099 10 
Total Electronic Pressure (GPa) -1.42098 10 
Total Electronic Pressure (GPa) -1.38824 10 
Pressure of Nuclei (GPa) 0.00163 10 
Pressure Total (GPa) -1.38661 10 

Can you please let me know what is this output about? (I have attached the 
output file.) 

Thanking you, 
Best regards, 
Krishnendu 





si2.ensemble-dyn.out
Description: Binary data
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[QE-users] can i use this trick to do faster MD calculation using pw.x ?

[KRISHNENDU MUKHERJEE]

Dear Prof. Kazume Nishidate, 

Is not that if we know the system is metallic glass then gamma-point 
calculation is the only possibility. I mean one can always go ahead with the 
minimum triclinic symmetry. But as the system in metallic glass then the 
enthalpy values for calculation considering triclinic symmetry can be higher ( 
as compared to gamma-point calculation). Kindly let me know your suggestions. 

Thanking you, 
Best regards, 
Krishnendu 

 

Dear Jayraj;

> the temperature fluctuations are too high compared to the other > literature. 
> Because you are using "thousands of atoms" in LAMMPS while you are using
only the 128 atoms in QE.

> MD simulation of thousands of atoms in LAMMPS …….
> On my metallic system, which has 128 atoms, You must understand the concept 
> of ensemble average.
A good text was introduced by Nicola:

> 3) not sure where to start - you need to learn and understand MD - a > good 
> start is if you google "ercolessi md primer" In addition to his elemental 
> comments, I want to add some trivial
things.

> "conv_thr" (i.e. ecutwfc=5 or 10) below a minimum cutoff of > 
> pseudopotential? So that I can get the next ionic position very Suppose you 
> have a potential curvature having a shape like a cup and 
a ball is falling along its curvature from its edge. The ball will
perform oscillating behavior continually if there is no energy loss by
a friction (energy conservation).

In a primitive molecular dynamics calculation (MD), total energy
(kinetic+potential) must be preserved in the long time scale (say
1 time steps) when the system does not have a restriction on its
kinetics (like temperature regulation). 

The "ecutwfc=5" apparently insufficient to evaluate the potential
curvature and hence your MD calculation will collapse. It is 
equivalent to a MD in LAMMPS with random interaction potentials.

Use the default cutoff energy and monitor the fluctuation of total
energies in the MD runs with changing the dt (time increment value) to
find the appropriate (largest) dt with preserving the total energies.

And you can also consider a gamma-point only calculation if your 
system is large enough.



西館数芽
Kazume NISHIDATE Ph.D

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN 


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[QE-users] Quantum Entanglement

[KRISHNENDU MUKHERJEE]

Dear members, 

Does the correlation function take care of quantum entanglement of electron 
wave-functions ? 

Thank you, 
Regards, 
Krishnendu 

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[QE-users] ATOMIC_POSITIONS input

[KRISHNENDU MUKHERJEE]

Dear users, 

Can I input the ATOMIC_POSITIONS from a separate text file? 

Regards, 
Krishnendu 

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[QE-users] pwscf, dielectric function and q-points

[KRISHNENDU MUKHERJEE]

Dear qe-users, 



When we do pwscf calculation for metals the dielectric function is also 
evaluated. The dielectric function is evaluated at general wavevector q. In 
that case why we are not inputing the q-points as we do for the ph.x code? 



Regards, 

Krishnendu, 

Principal Scientist, 

CSIR-NML, India. 

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[QE-users] Electronic band structure calculation for each q in ph.x

[KRISHNENDU MUKHERJEE]

Dear pw-user, 




I note that during ph.x calculation, electronic band structure is calculated 
for each q. Can you please let me know why? I guess the probable reason could 
be that, it is important to know the Fermi energy surface to calculate the 
phonon dispersion. 




Thank you, 

Regards, 

Krishnendu Mukherjee, Ph.D., 

Principal Scientist, 

CSIR-NML, 

India. 

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Re: [QE-users] meaning of Sym.Ops. (with q -> -q+G )

[KRISHNENDU MUKHERJEE]

Thank you Paolo for the explanation.

Regards,
Krishnendu

- Original Message -
From: "paolo giannozzi" 
To: users@lists.quantum-espresso.org
Cc: "KRISHNENDU MUKHERJEE" 
Sent: Sunday, February 26, 2023 1:34:53 PM
Subject: Re: [QE-users] meaning of Sym.Ops. (with q -> -q+G )

On 23/02/2023 11:56, KRISHNENDU MUKHERJEE wrote:

> 3 Sym.Ops. (with q -> -q+G )

> Can you please let me know what does Sym.Ops. (with q -> -q+G ) mean?

it means that there is a symmetry operation that sends q into -q+G, 
where G is a reciprocal-lattice vector

Paolo
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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[QE-users] meaning of Sym.Ops. (with q -> -q+G )

[KRISHNENDU MUKHERJEE]

Dear pw-user, 




While running the ph.x code I am getting the following in the output: 




Computing dynamical matrix for 

q = ( 0.000 0.000 0.000 ) 




3 Sym.Ops. (with q -> -q+G ) 




Can you please let me know what does Sym.Ops. (with q -> -q+G ) mean? 




Thank you, 

Regards, 

Krishnendu Mukherjee, Ph.D., 




Principal Scientist, 

CSIR-NML, 

India. 

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Re: [QE-users] q in the star : dynamical matrix and Bravais Lattice

[KRISHNENDU MUKHERJEE]

Dear Community, 

I found some answer to my last question from Stefano Baroni’s lecture on DFPT 
and also practicing thermo_pw/examples/example04. 
>From the lecture I came to know only one atom is perturbed. From the 
>practicing the example I came to know that symmetry comes into play to 
>determine q-points. But there is another parameter, “q in the star”. Can you 
>please let me know about this parameter? 

Thank you, 
Regards, 
Krishnendu 

--
 

[QE-users] dynamical matrix and Bravais Lattice 

Dear Community, 




For calculating the dynamical matrix when displacements are applied to the I 
and Jth atoms, do those displacements depend on the Bravais Lattice of the 
input atomic structure? 




Regards, 

Krishnendu 


-- next part -- 
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[QE-users] dynamical matrix and Bravais Lattice

[KRISHNENDU MUKHERJEE]

Dear Community, 




For calculating the dynamical matrix when displacements are applied to the I 
and Jth atoms, do those displacements depend on the Bravais Lattice of the 
input atomic structure? 




Regards, 

Krishnendu 


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Re: [QE-users] Symmetry identification difference between QE versions

[KRISHNENDU MUKHERJEE]

 Thank you Paolo for your kind reply and discussion. I would also thank Shimin 
Zhang for putting up the question so nicely. I also had those questions for 
some time.

- Original Message -
From: "paolo giannozzi" 
To: users@lists.quantum-espresso.org
Cc: "KRISHNENDU MUKHERJEE" 
Sent: Sunday, February 12, 2023 11:29:57 PM
Subject: Re: [QE-users] Symmetry identification difference between QE versions

On 12/02/2023 14:08, KRISHNENDU MUKHERJEE wrote:

> If some of the symmetry operators are missed, may be the shape and the 
> size of the Brillouin Zone can change. 

only if you perform structural optimization, and if your system does not 
like the initial symmetry

Paolo

> Can that have an effect on the scf energy calculation?
> 
> Thank you,
> Regards,
> Krishnendu
> 
> 
> On 11/02/2023 00:17, Shimin Zhang via users wrote:
> 
>  > My question is what could be the factor to cause this arbitrary symmetry
>  > identification?
> 
> small numerical differences between the true symmetric coordinates and
> axis and the almost symmetrical ones you have
> 
>  > What is the difference between these two versions of QE in the sense of
>  > identifying the symmetry?
> 
> nothing important, but it is hard to say more: much may have happened in
> the almost 4 years since v.6.4 was released
> 
>  > What is the consequence if some symmetry operators are missed?
> 
> more k-points used
> 
>  > Can I input the symmetry myself?
> 
> yes, with space groups and Wyckoff positions, but for a supercell it may
> be annoying
> 
> Paolo
> 
>  > Best,
>  > Shimin Zhang
>  > PhD student  in University of California, Santa Cruz
>  >
> 
> 
> 
> 
> 
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> 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
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> https://lists.quantum-espresso.org/mailman/listinfo/users

-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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[QE-users] Symmetry identification difference between QE versions

[KRISHNENDU MUKHERJEE]

Dear Paolo, 

If I could continue further with the discussion. 

> > What is the consequence if some symmetry operators are missed? 

> more k-points used 

If some of the symmetry operators are missed, may be the shape and the size of 
the Brillouin Zone can change. Can that have an effect on the scf energy 
calculation? 

Thank you, 
Regards, 
Krishnendu 


On 11/02/2023 00:17, Shimin Zhang via users wrote: 

> My question is what could be the factor to cause this arbitrary symmetry 
> identification? 

small numerical differences between the true symmetric coordinates and 
axis and the almost symmetrical ones you have 

> What is the difference between these two versions of QE in the sense of 
> identifying the symmetry? 

nothing important, but it is hard to say more: much may have happened in 
the almost 4 years since v.6.4 was released 

> What is the consequence if some symmetry operators are missed? 

more k-points used 

> Can I input the symmetry myself? 

yes, with space groups and Wyckoff positions, but for a supercell it may 
be annoying 

Paolo 

> Best, 
> Shimin Zhang 
> PhD student in University of California, Santa Cruz 
> 



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[QE-users] Unit for d2k0 from ev.x

[KRISHNENDU MUKHERJEE]

Dear Community, 

When I run the ev.x I got the value for d2k0. Is it the second pressure 
derivative of bulk modulus? Can you please let me know the unit of it? 

Regards, 
Krishnendu 

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[QE-users] local-TF mixing_mode and supercell of random binary solid solution

[KRISHNENDU MUKHERJEE]

Dear Community, 

Is it appropriate to use mixing_mode = ‘local-TF’ , in case of a supercell 
containing two different type of atoms. (The supercell would be Special 
Quasi-random structure (SQS) for random binary solid solution). 
I have started to use the mixing_mode = ‘local-TF’ and it is giving better 
convergence as compared to the default mixing_mode. 

Regards, 
Krishnendu 


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[QE-users] Quantume Espresso 6.1, 6.4.1, 6.5

[KRISHNENDU MUKHERJEE]

Dear Community, 

For some reason I have to use QE 6.1 now. But I have done some calculations 
before, for my materials system using QE 6.4.1 and QE 6.5. Will the simulations 
done using QE 6.1 comparable with my previous simulations done using QE 6.4.1 
and QE 6.5 ? 


Regards, 
Krishnendu 

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[QE-users] pw.x, Green function method, finite size

[KRISHNENDU MUKHERJEE]

Dear Lorenzo Paulatto, 

Thank you for your reply. I am replying with a separate thread. Of course 
surface effects can put a question mark for the approach. The following 
article, “A Reduction in Particle Size Generally Causes Body-Centered-Cubic 
Metals to Expand but Face-Centered-Cubic Metals to Contract” concludes that the 
metal to metal bond length decreases from center to the surface as well as the 
co-ordination number. 

But if the nano-grain size is bigger say in the range of 50 nm then may be the 
effect of surface will be decreased (in the above mentioned article the cluster 
size is less than 2 nm). Nevertheless, I am willing to take up the study in the 
near future. This approach would have the additional benefit that if the 
nano-grain experiences a negative hydrostatic pressure due to significant 
volume of grain-boundary present that can be added to the unit-cell. 

Best regards, 
Krishnendu 


 

[QE-users] Phonon Dispersion of graphene 
PAULATTO Lorenzo lorenzo.paulatto at cnrs.fr 
Sun Dec 25 16:22:02 CET 2022 
• Previous message: [QE-users] Phonon Dispersion of graphene 
• Next message: [QE-users] Out of memory in spin-polarized calculations? 
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 
 
Maybe one could do something, i.e. Wannier functions are not too dissimilar 
from force constants. But would the effect of the surface properly taken into 
account? These are not simple questions, a proper study takes years, and starts 
with reading the available literature (which I have not done) 
Hth 

 
From: users  on behalf of 
KRISHNENDU MUKHERJEE  
Sent: Sunday, December 25, 2022 3:49:35 PM 
To: users 
Subject: [QE-users] Phonon Dispersion of graphene 


Dear Lorenzo Paulatto, 

Can the finite size as a perturbation with Green function methods be added to 
pw.x calculations too ? For example can the Self-consistent field energy 
calculated for unit cell be modified with the Green function methods to that of 
a finite sized crystal ? 

Regards, 
Krishnendu 

--- 

[QE-users] Phonon Dispersion of graphene 
PAULATTO Lorenzo lorenzo.paulatto at cnrs.fr 
Sat Dec 24 11:30:59 CET 2022 
• Previous message: [QE-users] Phonon Dispersion of graphene 
• Next message: [QE-users] Out of memory in spin-polarized calculations? 
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 
 
Dear Jahid, you have to decide precisely what you want, than you may be able to 
simulate it in different ways. A width of 10nm is probably too large for a 
direct DFT calculation of phonons, in this case you can use the phonons for the 
unit cell and add the finite size as a perturbation with Green function 
methods. I know a paper where this is done, but there are probably others, and 
other methods. https://hal.archives-ouvertes.fr/hal-03011389 


Hth 


LP 
 
From: users  on behalf of Md. 
Jahid Hasan Sagor  
Sent: Saturday, December 24, 2022 10:17:28 AM 
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] Phonon Dispersion of graphene 

Hi, 

Please help if you can. I am trying to find out the dispersion relation of 
graphene. I know that to find out the relation I have to use pw.x, ph.x, q2r.x 
and matdyn.x. But the problem is, after applying all the packages, I might get 
a phonon dispersion relation of graphene which is infinitely long in x and y 
direction. However, in my model I am using a finite width of graphene around 
10nm (24 unit cell in the vertical direction). Which command in QE can do this 
for me so that I can model a graphene which is infinitely long in x direction 
and 10 nm in y direction? 

Best Regards 
Md Jahid Hasan 
-- next part -- 




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[QE-users] Phonon Dispersion of graphene

[KRISHNENDU MUKHERJEE]

Dear Lorenzo Paulatto, 

Can the finite size as a perturbation with Green function methods be added to 
pw.x calculations too ? For example can the Self-consistent field energy 
calculated for unit cell be modified with the Green function methods to that of 
a finite sized crystal ? 

Regards, 
Krishnendu 

--- 

> On 25 Dec 2022, at 00:26, Md. Jahid Hasan Sagor < [ 
> https://lists.quantum-espresso.org/mailman/listinfo/users | md.sagor at 
> maine.edu ] > wrote: > > > Then why would the calculation be considered 
> computationally large if I define 10 nm width ( rather I reduce my system 
> size from infinite to 10 nm)? Can you explain it to me? Because “reducing the 
> size” (actually, making it finite) would break translational symmetry and 
> thus prevent us from using the Bloch theorem. In an infinite *and periodic* 
> system, Bloch theorem allows us to break an infinite-dimensional Hamiltonian 
> matrix into an infinite number of finite-dimensional matrices (one for every 
> k vector), which can be easily diagonalized one by one. This is not possible 
> in a finite system (or in an infinite and aperiodic one, for that matter). 
> So, surprisingly (or not so surprisingly once you understand the maths) 
> finite systems may be computationally harder than some infinite ones. Stefano 
> B

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http://stefano.baroni.me ] 






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[QE-users] Phonon Dispersion of graphene ] 



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[QE-users] nosym=.TRUE., input k-points and CELL_PARAMETERS

[KRISHNENDU MUKHERJEE]

Dear QE community, 

If I use the nosym = .TRUE. option, then should I give the input 
CELL_PARAMETERS also in correspondence with the input k-points. For example, if 
I give the input k-points that of Irreducible Brillouin Zone of FCC, should I 
also input the lattice CELL_PARAMETERS of that of a FCC primitive supercell, 
that is, for example, 
2.00 2.00 0.00 
2.00 0.00 2.00 
0.00 2.00 2.00 
(64 atoms) 

I am interested in SCF calculation of a hypothetical FCC random/disordered 
solid solution of type A_B. 

Regards, 
Krishnendu 


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[QE-users] Parallelization and Input/Output of wfc in QE

[KRISHNENDU MUKHERJEE]

Dear Dr. Pietro, 

Kindly ignore my last message. I am able to see the equations by clicking at 
the links given in the end of your post. 

Regards, 
Krishnendu 


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[QE-users] Parallelization and Input/Output of wfc in QE

[KRISHNENDU MUKHERJEE]

Dear Dr. Pietro, 

Thank you for your reply. I am sorry that I am not able to see the Figures. Can 
you kindly repost them or I am not able to see them as I am just clicking the 
link which is redirecting to the Quantum Espressso forum page. 

Regards, 
Krishnendu 
--
 

Hello 

To obtain the projected density of states for a particular atomic orbital you 
calculate a weighted density of states , using as weight the square modulus of 
the 
projection of the wave-function to the atomic orbital. In quantum-espresso this 
is done with the program projwfc.x 

So normal DOS is 

[cid:image001.png at 01D9055B.40F9B610] 

The projected density of states is 

[cid:image002.png at 01D9055C.483BD0B0] 

Hope this helps 
Best regards, Pietro 

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 

From: KRISHNENDU MUKHERJEE<mailto:krishnendu at nmlindia.org> 
Sent: Wednesday, November 30, 2022 11:23 AM 
To: users<mailto:users at lists.quantum-espresso.org> 
Subject: [QE-users] Parallelization and Input/Output of wfc in QE 


Dear Dr. Pietro, 

Thank you for your reply. I did not have a course on Quantum Mechanics and 
Solid State Physics. But I am currently reading thoroughly text books on those 
subjects. I have another question. 
In Quantum Espresso the electron is considered to be described by plane-waves. 
So, it does not have information regarding its belongness to any particular s,p 
or d orbital. However, I have seen articles with Quantum Espresso results with 
DOS for a particular orbital (e.g., 3d). Can you kindly let me know how DOS of 
a particular orbital can be obtained from the plane-wave representation of 
electron? 

Thank you, 
Best regards, 
Krishnendu 


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[QE-users] Parallelization and Input/Output of wfc in QE

[KRISHNENDU MUKHERJEE]

Dear Dr. Pietro, 

Thank you for your reply. I did not have a course on Quantum Mechanics and 
Solid State Physics. But I am currently reading thoroughly text books on those 
subjects. I have another question. 
In Quantum Espresso the electron is considered to be described by plane-waves. 
So, it does not have information regarding its belongness to any particular s,p 
or d orbital. However, I have seen articles with Quantum Espresso results with 
DOS for a particular orbital (e.g., 3d). Can you kindly let me know how DOS of 
a particular orbital can be obtained from the plane-wave representation of 
electron? 

Thank you, 
Best regards, 
Krishnendu 

---
 

Dear Krishnendu, 

if you want to know what the grids are (those appearing in the header of 
the table) check this message from Stefano de Gironcoli: 

https://lists.quantum-espresso.org/pipermail/developers/2017-November/001783.html
 

The second keyword in that table is "sticks", which concerns with the 
way the data is distributed among multiple processes in order to perform 
a parallel FFT. This presentation, again by Prof. de Gironcoli, will 
explain how that works: 

https://www.youtube.com/watch?v=YqYdu1aVi-o 

With these information and the details of your input file (ecutwfc, 
ecutrho and the lattice) you should be able to roughly predict the 
number of G-vectors of the various grids of your plane wave expansion. 
Predicting the number of sticks is slightly more complicated and, in my 
opinion, it's quite pointless. 

Best wishes, 
Pietro 

--- 

Pietro Bonfà 
Università di Parma 


On 11/29/22 12:56, KRISHNENDU MUKHERJEE wrote: 
> 
> How many G-vectors are required to describe a plane-wave ? 
> 
> It will be very helpful if I could understand the following part of the 
> output that I am getting almost in the beginning. 
> 
> G-vector sticks info 
>  
> sticks: dense smooth PW G-vecs: dense smooth PW 
> Sum 6181 3093 885 364637 128843 20341 
> 
> Thank you, 
> Regards, 
> 
> Krishnendu 
> 
> --
>  
> 
> Actually, all the coefficients of all the wavefunctions AT A GIVEN K 
> POINT: there is one wavefunction file per k point. 
> 
> Paolo 
> 
> On 11/28/22 14:07, Riccardo Piombo uniroma1 via users wrote: 
>>/So in a single file QE stores ALL the coefficients of ALL the wfcs? />//>/Is 
>>it correct? />//>//>/Thanks for your help, />//>/Riccardo Piombo />// 




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[QE-users] Parallelization and Input/Output of wfc in QE

[KRISHNENDU MUKHERJEE]

How many G-vectors are required to describe a plane-wave ? 

It will be very helpful if I could understand the following part of the output 
that I am getting almost in the beginning. 

G-vector sticks info 
 
sticks: dense smooth PW G-vecs: dense smooth PW 
Sum 6181 3093 885 364637 128843 20341 

Thank you, 
Regards, 

Krishnendu 

--
 
Actually, all the coefficients of all the wavefunctions AT A GIVEN K 
POINT: there is one wavefunction file per k point.

Paolo

On 11/28/22 14:07, Riccardo Piombo uniroma1 via users wrote:
> So in a single file QE stores ALL the coefficients of ALL the wfcs? > > Is it 
> correct? > > > Thanks for your help, > > Riccardo Piombo > 

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[QE-users] CPMD simualtion of metallic alloys upto 4 ps but RDF g(r) is not getting smooth

[KRISHNENDU MUKHERJEE]

Dear Jayraj Anadani, 

As far as I remember yours AIMD calculation was for 54 Zr_Cu atoms which was in 
the form of a cluster inside vacuum in a box. But I guess the LAMMPS simulation 
is for a Supercell, that is, there is no vacuum. So, in case of AIMD the atoms 
see a surface while for the LAMMPS calculation there is no surface. So, I guess 
there is a difference between your AIMD and LAMMPS simulations. 

Regards, 
Krishnendu 

--
 
On Mon, 7 Nov, 2022, Jayraj Anadani wrote: 


Thank you sir 

On Mon, 7 Nov, 2022, 7:04 pm Kazume NISHIDATE,  
wrote: 

> Dear Jayraj Anadani 
> 
> > AIMD procedure, i am only taking 54 atomic supercell according to 
> > CPMD procedure. And also , for taking 'one MD step' of 1 atoms 
> 
> Than, take the time averaged RDF of the cp.x calculation, 1000 to 
> 2000 MD steps may be enough. You can get a smooth RDF graph thanks 
> to the 'Ergodic theory'. 
> 
> 
> 
> 西館数芽 
> Kazume NISHIDATE Ph.D 



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Re: [QE-users] Comparison of k_points for two different inputs of BCC structure

[KRISHNENDU MUKHERJEE]

Hello Xin, 

Thank you for your reply. Sorry for the late reply from my side. Below is the 
k-points obtained from kpoints.x for Simple Cubic Bravais Lattice, for a 4 4 4 
0 0 0 mesh, considering the 48 symmetries. Let’s call it Table 4. 

TABLE 4 
10 
1 0.000 0.000 0.000 1.00 
2 0.250 0.000 0.000 6.00 
3 0.500 0.000 0.000 3.00 
4 0.250 0.250 0.000 12.00 
5 0.500 0.250 0.000 12.00 
6 0.500 0.500 0.000 3.00 
7 0.250 0.250 0.250 8.00 
8 0.500 0.250 0.250 12.00 
9 0.500 0.500 0.250 6.00 
10 0.500 0.500 0.500 1.00 

If you multiply the weights of your k_points with 32 you will get the weights 
as in Table 4. I guess the k_points are different as your 
//CELL_PARAMETERS were given as {alat}// 
> // 3.0 0.0 0.0// 
> // 0.0 3.0 0.0// 
> // 0.0 0.0 3.0 // 

If you have your cell_parameters as 
1 0 0 
0 1 0 
0 0 1 
You would have got the values of k_points of Table 4. May be you have to add 1 
to match the sign. 
So may be with your input script the energy calculations are done for the 
k_points of a Simple Cubic Bravais Lattice. However, I guess you may want the 
k_points for a BCC Bravais Lattice. 

Thanking you, 
Best regards, 
Krishnendu 



From: "xin tlg jin"  
To: "KRISHNENDU MUKHERJEE"  
Cc: users@lists.quantum-espresso.org 
Sent: Monday, October 31, 2022 5:28:30 PM 
Subject: Re: Comparison of k_points for two different inputs of BCC structure 

Hello Krishnendu, 

I saw there are k-points given by the output of pw.x: 

number of k points= 10 Methfessel-Paxton smearing, width (Ry)= 0.0600 
cart. coord. in units 2pi/alat 
k( 1) = ( 0.000 0.000 0.000), wk = 0.0312500 
k( 2) = ( 0.000 0.000 0.083), wk = 0.1875000 
k( 3) = ( 0.000 0.000 -0.167), wk = 0.0937500 
k( 4) = ( 0.000 0.083 0.083), wk = 0.375 
k( 5) = ( 0.000 0.083 -0.167), wk = 0.375 
k( 6) = ( 0.000 -0.167 -0.167), wk = 0.0937500 
k( 7) = ( 0.083 0.083 0.083), wk = 0.250 
k( 8) = ( 0.083 0.083 -0.167), wk = 0.375 
k( 9) = ( 0.083 -0.167 -0.167), wk = 0.1875000 
k( 10) = ( -0.167 -0.167 -0.167), wk = 0.0312500 



But I am not sure how to exactly compare to the k-points generated by you. 
However if you are interested, I think you can generate the list of k-points 
from my input. of My input is at the end of the email. 

Thank you. 

Best regards, 
Xin 

On 31/10/2022 12:24, KRISHNENDU MUKHERJEE wrote: 




Hello Xin, 

Thank you for your reply. I have made a new thread. Below is the k-points 
obtained from kpoints.x for BCC Bravais Lattice, for a 4 4 4 0 0 0 mesh, 
considering the 48 symmetries. I hope this will be the same for the case with 
calculations for ibrav=3, with BCC primitive cell with one atom per cell. 
8 (=number of k_points) 

1 0.000 0.000 0.000 1.00 
2 0.250 0.000 0.250 12.00 
3 0.500 0.000 0.500 6.00 
4 0.250 0.250 0.500 24.00 
5 0.000 0.000 0.500 6.00 
6 0.250 0.000 0.750 12.00 
7 -0.500 0.500 0.500 2.00 
8 0.000 0.000 1.000 1.00 


Now let us compare with the k_points that were used in your calculation when a 
BCC supercell consisting of BCC Unit Cells is used as input with ibrav=0. So, I 
request you if you can kindly post the k_points considered in your calculation. 
Also you may kindly include your input script once more so that later on 
somebody can follow the discussion. 

Thanking you, 
Best regards, 
Krishnendu 



From: "xin tlg jin" [ mailto:xin.tlg@outlook.com | 
 ] 
To: [ mailto:users@lists.quantum-espresso.org | 
users@lists.quantum-espresso.org ] 
Cc: "KRISHNENDU MUKHERJEE" [ mailto:krishne...@nmlindia.org | 
 ] 
Sent: Monday, October 31, 2022 12:28:24 PM 
Subject: Re: [QE-users] Parallel computing of QE7.1 vc-relax crashes when using 
large number of processors 

Hello Krishnendu, 

Thank you for the message 
Yes, we can start a separate thread. I didn't realize that there could be such 
a problem. 
Actually, the reason that I use ibrav=0 for BCC W is that I want to put some 
interstitials inside if the program works. 

Best regards, 
Xin 


On 30/10/2022 05:35, KRISHNENDU MUKHERJEE wrote: 

BQ_BEGIN


Dear Xin Jin, 

Sorry that I have another matter to discuss. If you wish we may start a 
separate thread on the subject I am eager to discuss. I have some concern about 
your script. If you want to do calculation for BCC W you may need to use 
ibrav=3. Note that for ibrav=3 the (primitive) lattice vectors are in the form: 

ibrav=3 cubic I (bcc) 
v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1) which is inbuilt in 
QE (so that you need not input CELL_PARAMETERS) and you only need to put an 
atom in the position 0.00 0.00 0.00. 
With those input QE determines the k_points for BCC Bravais Lattice. 

You

[QE-users] Comparison of k_points for two different inputs of BCC structure

[KRISHNENDU MUKHERJEE]

Hello Xin, 

Thank you for your reply. I have made a new thread. Below is the k-points 
obtained from kpoints.x for BCC Bravais Lattice, for a 4 4 4 0 0 0 mesh, 
considering the 48 symmetries. I hope this will be the same for the case with 
calculations for ibrav=3, with BCC primitive cell with one atom per cell. 
8 (=number of k_points) 

1 0.000 0.000 0.000 1.00 
2 0.250 0.000 0.250 12.00 
3 0.500 0.000 0.500 6.00 
4 0.250 0.250 0.500 24.00 
5 0.000 0.000 0.500 6.00 
6 0.250 0.000 0.750 12.00 
7 -0.500 0.500 0.500 2.00 
8 0.000 0.000 1.000 1.00 


Now let us compare with the k_points that were used in your calculation when a 
BCC supercell consisting of BCC Unit Cells is used as input with ibrav=0. So, I 
request you if you can kindly post the k_points considered in your calculation. 
Also you may kindly include your input script once more so that later on 
somebody can follow the discussion. 

Thanking you, 
Best regards, 
Krishnendu 



From: "xin tlg jin"  
To: users@lists.quantum-espresso.org 
Cc: "KRISHNENDU MUKHERJEE"  
Sent: Monday, October 31, 2022 12:28:24 PM 
Subject: Re: [QE-users] Parallel computing of QE7.1 vc-relax crashes when using 
large number of processors 

Hello Krishnendu, 

Thank you for the message 
Yes, we can start a separate thread. I didn't realize that there could be such 
a problem. 
Actually, the reason that I use ibrav=0 for BCC W is that I want to put some 
interstitials inside if the program works. 

Best regards, 
Xin 


On 30/10/2022 05:35, KRISHNENDU MUKHERJEE wrote: 




Dear Xin Jin, 

Sorry that I have another matter to discuss. If you wish we may start a 
separate thread on the subject I am eager to discuss. I have some concern about 
your script. If you want to do calculation for BCC W you may need to use 
ibrav=3. Note that for ibrav=3 the (primitive) lattice vectors are in the form: 

ibrav=3 cubic I (bcc) 
v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1) which is inbuilt in 
QE (so that you need not input CELL_PARAMETERS) and you only need to put an 
atom in the position 0.00 0.00 0.00. 
With those input QE determines the k_points for BCC Bravais Lattice. 

You have input the atomic positions in terms of supercell made of BCC unit 
cell. And you have put ibrav=0. With those input I am afraid most probably the 
k_points generated would be that of a Simple Cubic structure. 
What we can do is next week I would generate the k_points for BCC with a mesh 
of 4 4 4 0 0 0 and post it. And you can see whether it is matching with the 
k_points considered in your calculation and discuss further. 

Thank you, 
Best regards, 
Krishnendu 

--
 

Xin Jin wrote on 28/Oct/2022 


Dear Quantum Espresso Forum, 

I encountered a problem related to the parallel computing using QE7.1 
for vc-relax. 

I was trying to perform a vc-relax for a 3*3*3 BCC tungsten super cell. 
The code works fine for non-parallel computing, also works fine for 
parallel computing if the number of processors is smaller than 10. 

However, if the number of processors is larger than 10, I will get 
following MPI error: 
/*** An error occurred in MPI_Comm_free// 
//*** reported by process [3585895498,2]// 
//*** on communicator MPI_COMM_WORLD// 
//*** MPI_ERR_COMM: invalid communicator// 
//*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,// 
//*** and potentially your MPI job)/ 

For parallel computing, I am using /OpenMPI/3.1.4-gcccuda/. (In 
addition, it seems that If I use OpenMPI V4, the simulation speed will 
be much slower than that of V3.) 

Another thing is that, if I decrease the size of the supper cell, for 
example to 2*2*2, then there is no problem in the parallel computing 
even if I use more than 30 processors. 

Could you help me look at this problem, please? 

The input for QE can be found below. 

Thank you in advance! 

Xin Jin 

/&control// 
// 
// calculation='vc-relax' // 
// restart_mode='from_scratch', // 
// prefix='W_relax', // 
// pseudo_dir="../../PP_files",// 
// outdir='./'// 
// 
// /// 
 
// 
// &system// 
// ibrav= 0, // 
// celldm(1)=5.972,// 
// nat= 54, // 
// ntyp= 1,// 
// ecutwfc = 50,// 
// ecutrho = 500,// 
// occupations='smearing', smearing='mp', degauss=0.06// 
// /// 
// 
// &electrons// 
// diagonalization='david',// 
// conv_thr = 1.0d-8,// 
// mixing_beta = 0.5,// 
// /// 
 
// &ions// 
// /// 
// 
// &cell// 
// press = 0.0,// 
// /// 
 
//ATOMIC_SPECIES// 
// W 183.84 W.pbe-spn-kjpaw_psl.1.0.0.UPF// 
 
//CELL_PARAMETERS {alat}// 
// 3.0 0.0 0.0// 
// 0.0 3.0 0.0// 
// 0.0 0.0 3.0 // 
 
//ATOMIC_POSITIONS {alat}// 
//W 0.0 0.0 0.0// 
//

[QE-users] Parallel computing of QE7.1 vc-relax crashes when using large number of processors

[KRISHNENDU MUKHERJEE]

Dear Xin Jin, 

Sorry that I have another matter to discuss. If you wish we may start a 
separate thread on the subject I am eager to discuss. I have some concern about 
your script. If you want to do calculation for BCC W you may need to use 
ibrav=3. Note that for ibrav=3 the (primitive) lattice vectors are in the form: 

ibrav=3 cubic I (bcc) 
v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1) which is inbuilt in 
QE (so that you need not input CELL_PARAMETERS) and you only need to put an 
atom in the position 0.00 0.00 0.00. 
With those input QE determines the k_points for BCC Bravais Lattice. 

You have input the atomic positions in terms of supercell made of BCC unit 
cell. And you have put ibrav=0. With those input I am afraid most probably the 
k_points generated would be that of a Simple Cubic structure. 
What we can do is next week I would generate the k_points for BCC with a mesh 
of 4 4 4 0 0 0 and post it. And you can see whether it is matching with the 
k_points considered in your calculation and discuss further. 

Thank you, 
Best regards, 
Krishnendu 

--
 

Xin Jin wrote on 28/Oct/2022 


Dear Quantum Espresso Forum, 

I encountered a problem related to the parallel computing using QE7.1 
for vc-relax. 

I was trying to perform a vc-relax for a 3*3*3 BCC tungsten super cell. 
The code works fine for non-parallel computing, also works fine for 
parallel computing if the number of processors is smaller than 10. 

However, if the number of processors is larger than 10, I will get 
following MPI error: 
/*** An error occurred in MPI_Comm_free// 
//*** reported by process [3585895498,2]// 
//*** on communicator MPI_COMM_WORLD// 
//*** MPI_ERR_COMM: invalid communicator// 
//*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,// 
//*** and potentially your MPI job)/ 

For parallel computing, I am using /OpenMPI/3.1.4-gcccuda/. (In 
addition, it seems that If I use OpenMPI V4, the simulation speed will 
be much slower than that of V3.) 

Another thing is that, if I decrease the size of the supper cell, for 
example to 2*2*2, then there is no problem in the parallel computing 
even if I use more than 30 processors. 

Could you help me look at this problem, please? 

The input for QE can be found below. 

Thank you in advance! 

Xin Jin 

/&control// 
// 
// calculation='vc-relax' // 
// restart_mode='from_scratch', // 
// prefix='W_relax', // 
// pseudo_dir="../../PP_files",// 
// outdir='./'// 
// 
// /// 
 
// 
// &system// 
// ibrav= 0, // 
// celldm(1)=5.972,// 
// nat= 54, // 
// ntyp= 1,// 
// ecutwfc = 50,// 
// ecutrho = 500,// 
// occupations='smearing', smearing='mp', degauss=0.06// 
// /// 
// 
// &electrons// 
// diagonalization='david',// 
// conv_thr = 1.0d-8,// 
// mixing_beta = 0.5,// 
// /// 
 
// &ions// 
// /// 
// 
// &cell// 
// press = 0.0,// 
// /// 
 
//ATOMIC_SPECIES// 
// W 183.84 W.pbe-spn-kjpaw_psl.1.0.0.UPF// 
 
//CELL_PARAMETERS {alat}// 
// 3.0 0.0 0.0// 
// 0.0 3.0 0.0// 
// 0.0 0.0 3.0 // 
 
//ATOMIC_POSITIONS {alat}// 
//W 0.0 0.0 0.0// 
//W 0.5 0.5 0.5// 
//W 1.0 0.0 0.0// 
//W 1.5 0.5 0.5// 
//W 2.0 0.0 0.0// 
//W 2.5 0.5 0.5// 
//W 0.0 1.0 0.0// 
//W 0.5 1.5 0.5// 
//W 1.0 1.0 0.0// 
//W 1.5 1.5 0.5// 
//W 2.0 1.0 0.0// 
//W 2.5 1.5 0.5// 
//W 0.0 2.0 0.0// 
//W 0.5 2.5 0.5// 
//W 1.0 2.0 0.0// 
//W 1.5 2.5 0.5// 
//W 2.0 2.0 0.0// 
//W 2.5 2.5 0.5// 
//W 0.0 0.0 1.0// 
//W 0.5 0.5 1.5// 
//W 1.0 0.0 1.0// 
//W 1.5 0.5 1.5// 
//W 2.0 0.0 1.0// 
//W 2.5 0.5 1.5// 
//W 0.0 1.0 1.0// 
//W 0.5 1.5 1.5// 
//W 1.0 1.0 1.0// 
//W 1.5 1.5 1.5// 
//W 2.0 1.0 1.0// 
//W 2.5 1.5 1.5// 
//W 0.0 2.0 1.0// 
//W 0.5 2.5 1.5// 
//W 1.0 2.0 1.0// 
//W 1.5 2.5 1.5// 
//W 2.0 2.0 1.0// 
//W 2.5 2.5 1.5// 
//W 0.0 0.0 2.0// 
//W 0.5 0.5 2.5// 
//W 1.0 0.0 2.0// 
//W 1.5 0.5 2.5// 
//W 2.0 0.0 2.0// 
//W 2.5 0.5 2.5// 
//W 0.0 1.0 2.0// 
//W 0.5 1.5 2.5// 
//W 1.0 1.0 2.0// 
//W 1.5 1.5 2.5// 
//W 2.0 1.0 2.0// 
//W 2.5 1.5 2.5// 
//W 0.0 2.0 2.0// 
//W 0.5 2.5 2.5// 
//W 1.0 2.0 2.0// 
//W 1.5 2.5 2.5// 
//W 2.0 2.0 2.0// 
//W 2.5 2.5 2.5// 
// 
//K_POINTS {automatic}// 
//4 4 4 0 0 0// 
/ 
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[QE-users] reading output generated from Band.x

[KRISHNENDU MUKHERJEE]

Dear MD NILOY KHAN, 
Thank you for your question about the topic. Sorry, that I do not have answer 
to your question but have some questions. I work with FCC metals. I also see in 
the output: 

point group O_h (m-3m) 
there are 10 classes 
the character table: 

E 8C3 3C2 6C4 6C2' i 8S6 3s_h 6S4 6s_d 
A_1g 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 
A_2g 1.00 1.00 1.00 -1.00 -1.00 1.00 1.00 1.00 -1.00 -1.00 
E_g 2.00 -1.00 2.00 0.00 0.00 2.00 -1.00 2.00 0.00 0.00 
T_1g 3.00 0.00 -1.00 1.00 -1.00 3.00 0.00 -1.00 1.00 -1.00 
T_2g 3.00 0.00 -1.00 -1.00 1.00 3.00 0.00 -1.00 -1.00 1.00 
A_1u 1.00 1.00 1.00 1.00 1.00 -1.00 -1.00 -1.00 -1.00 -1.00 
A_2u 1.00 1.00 1.00 -1.00 -1.00 -1.00 -1.00 -1.00 1.00 1.00 
E_u 2.00 -1.00 2.00 0.00 0.00 -2.00 1.00 -2.00 0.00 0.00 
T_1u 3.00 0.00 -1.00 1.00 -1.00 -3.00 0.00 1.00 -1.00 1.00 
T_2u 3.00 0.00 -1.00 -1.00 1.00 -3.00 0.00 1.00 1.00 -1.00 

the symmetry operations in each class and the name of the first element: 

E 1 
identity 
8C3 17 19 20 18 24 21 22 23 
120 deg rotation - cart. axis [-1,-1,-1] 
3C2 2 4 3 
180 deg rotation - cart. axis [0,0,1] 
6C4 7 8 15 16 12 11 
90 deg rotation - cart. axis [0,0,-1] 
6C2' 5 6 14 13 10 9 
180 deg rotation - cart. axis [1,1,0] 
i 25 
inversion 
8S6 41 43 44 42 48 45 46 47 
inv. 120 deg rotation - cart. axis [-1,-1,-1] 
3s_h 26 28 27 
inv. 180 deg rotation - cart. axis [0,0,1] 
6S4 31 32 39 40 36 35 
inv. 90 deg rotation - cart. axis [0,0,-1] 
6s_d 29 30 38 37 34 33 
inv. 180 deg rotation - cart. axis [1,1,0] 

Can you kindly let me know what does the symbols A1_g, A_2g, E_g, T_1g, T_2g, 
A_1u, A_2u, E_u, T_1u, T_2u and E, 8C3, 3C2, 6C4, 6C2', i, 8S6,3s_h, 6S4, 6s_d 
mean. Can you kindly guide us to a reference textbook too? 
Thank you, 
Best regards, 
Krishnendu 


 

You wrote: 

what does number beside 2C6 or 2C3, C2 represent?? 
and in band symmetry information( Band symmetry, D_6h(6/mmm) point group: 
e( 1 - 1) = -47.33409 eV *1* --> ?) what does *1* & *2 * 
represent?? 
%%part of output file. 
the symmetry operations in each class and the name of the first element: 

E 1 

2C6 5 6 

2C3 7 8 

C2 2 

3C2' 4 12 11 

3C2'' 3 9 10 

i 13 

2S3 17 18 

2S6 19 20 

s_h 14 

3s_d 16 24 23 

3s_v 15 21 22 


Band symmetry, D_6h(6/mmm) point group: 

e( 1 - 1) = -47.33409 eV 1 --> ? 
e( 2 - 2) = -47.33365 eV 1 --> ? 
e( 3 - 3) = -47.28209 eV 1 --> A_1g 
e( 4 - 4) = -47.27869 eV 1 --> B_2u 
e( 5 - 5) = -47.26498 eV 1 --> ? 
e( 6 - 6) = -47.26205 eV 1 --> ? 
e( 7 - 7) = -19.26259 eV 1 --> A_1g 
e( 8 - 8) = -19.24575 eV 1 --> B_2u 
e( 9 - 9) = -19.20116 eV 1 --> A_2u 
e( 10 - 10) = -19.18887 eV 1 --> B_1g 
e( 11 - 12) = -19.16539 eV 2 --> ? 
e( 13 - 14) = -19.16451 eV 2 --> ? 
e( 15 - 16) = -19.11477 eV 2 --> E_2g 
e( 17 - 18) = -19.10279 eV 2 --> E_1u 
e( 19 - 20) = -19.09577 eV 2 --> E_1g 
e( 21 - 21) = -19.08469 eV 1 --> A_2u 
e( 22 - 22) = -19.07140 eV 1 --> B_1g 
e( 23 - 24) = -19.06663 eV 2 --> E_2u 
e( 25 - 25) = -16.14063 eV 1 --> A_1g 
e( 26 - 26) = -16.13636 eV 1 --> B_2u 
e( 27 - 28) = -16.10625 eV 2 --> ? 
e( 29 - 30) = -16.10447 eV 2 --> ? 
e( 31 - 32) = -16.10016 eV 2 --> E_2g 
e( 33 - 34) = -16.09696 eV 2 --> E_1u 
e( 35 - 35) = -4.71119 eV 1 --> A_1g 
e( 36 - 36) = -4.38281 eV 1 --> B_2u 
e( 37 - 37) = 2.67823 eV 1 --> B_1g 
e( 38 - 39) = 4.58984 eV 2 --> E_2g 
e( 40 - 41) = 4.95370 eV 2 --> E_1u 
e( 42 - 42) = 5.16461 eV 1 --> A_1g 
e( 43 - 43) = 5.34977 eV 1 --> A_2u 
e( 44 - 44) = 6.62402 eV 1 --> B_2u 
e( 45 - 46) = 8.48597 eV 2 --> E_1u 
e( 47 - 48) = 9.43270 eV 2 --> E_2g 
e( 49 - 49) = 9.56785 eV 1 --> B_1g 
e( 50 - 50) = 9.88685 eV 1 --> A_1g 

** 

** 

-- 
*Thanks & Regards* 
*MD NILOY KHAN* 
*Gmail: *khanniloy534 at gmail.com 
*Phone: *+8801735744576, +8801619141513 
*Address:* Nalua, Sakhipur, Tangail, Post Code: 1950 
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[QE-users] what is the unit of kpoint.x output

[KRISHNENDU MUKHERJEE]

Dear Youzhao Lan, 

I think it is in the unit of 2*pi/a. But I also have a question to the 
community that whether 'a' is as the unit lattice vector or as the primitive 
lattice vector depending on the Bravais Lattice. 

Thank you, 
Regards, 
Krishnendu 

-- 
Dear all, 
Could you tell me what the unit of kpoint.x output is? 

Best regards. 
 
Youzhao Lan 
College of Chemistry and Life Sciences, 
Zhejiang Normal University, 
Jinhua, Zhejiang, 
321004, China. 
 


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[QE-users] Different SCF energy when # of MPI is changed

[KRISHNENDU MUKHERJEE]

Dear Takahiro Chiba, 

Isn't that the degauss value should be in between 0.01 to 0.02 Rydberg. That is 
mentioned by Nicola Marzari in his lecture. 

Regards, 
Krishnendu 

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Re: [QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Thank you Paolo. I will try with a 64 atom Cu supercell and discuss the result 
in this forum.

Regards,
Krishnendu


- Original Message -
From: "paolo giannozzi" 
To: "KRISHNENDU MUKHERJEE" 
Cc: users@lists.quantum-espresso.org
Sent: Friday, October 7, 2022 6:57:39 PM
Subject: Re: [QE-users] Ensemble_DFT simulation

I would say that the limiting factor is the Gamma-only (k=0) sampling 
used by CP. The larger the supercell, the better the sampling. For a 
sufficiently large supercell of Cu, or similar 3D systems, there should 
be no special problems with ensemble DFT.

Paolo

On 07/10/2022 07:19, KRISHNENDU MUKHERJEE wrote:
> 
> Thank you Paolo. I have just a small follow up question. Is ensemble_DFT 
> suitable only for cluster inside vacuum in a box, or slab inside vacuum in a 
> box?
> Or, with very careful choice of inputs we can apply ensemble_DFT for 3D cases 
> too? For example; if I want to simulate a Cu supercell at 300 K?
> 
> Regards,
> Krishnendu
> 
> 
> - Original Message -
> From: "paolo giannozzi" 
> To: users@lists.quantum-espresso.org, "KRISHNENDU MUKHERJEE" 
> 
> Sent: Friday, October 7, 2022 2:14:38 AM
> Subject: Re: [QE-users] Ensemble_DFT simulation
> 
> Thank you for reporting this. Some examples have been run years ago and
> things have changed meanwhile
> 
> Paolo
> 
> On 06/10/2022 08:30, KRISHNENDU MUKHERJEE wrote:
>>
>> Dear Community,
>>
>> Few days back I wrote to this forum regarding the zero values of the
>> eigenvalues:
>>
>> --
>>
>> When I practised the example 08 given in CPV/examples, I got the note:
>>
>> NOTE : eigenvalues are not computed without ortho
>>
>> And the reported eigenvalues are all zeros.
>>
>> However, in the given reference output the note is not there. Also, the
>> eigen values are non-zero.
>>
>> Please suggest to solve the problem.
>>
>> ---
>>
>> To solve it, I think, one may do few steps of orthogonalization =
>> 'Gram-Schmidt', and then using the autopilot mode change it to
>> "orthogonalization = 'ortho'.
>>
>> By doing so, on_step 6, I got the values of the eigenvalues.
>>
>> In the reference example08, the eigenvalues at the end of step 5 were:
>>
>> Eigenvalues (eV), kp =1 , spin =1
>>
>> -9.73-8.12-3.55-2.45-2.45-1.20-1.200.82
>>
>> After Autopilot on_step 6, to orthogonalization = ‘ortho’, at the end of
>> 10 step the eigenvalues I got is:
>>
>> STEP:100.00
>>
>> Eigenvalues (eV), kp =1 , spin =1
>>
>> -9.75-8.13-3.56-2.46-2.46-1.21-1.210.93
>>
>> I hope in this way the cp.x runs with correct eigenvalues as compared to
>> what might be happening with orthogonalization = 'Gram-Schmidt',only.
>>
>> Thanking you,
>>
>> Regards,
>>
>> Krishnendu
>>
>>
>>
>>
>>
>> ___
>> 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 
>> (https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7C80a986d45d644f992b5b08daa8239aab%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638007168127521794%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4mFqbSMPI7EEum7z%2B02jvSRYvB4AsxultU1%2F0k9MwTg%3D&reserved=0)
>> users mailing list users@lists.quantum-espresso.org
>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=05%7C01%7Cpaolo.giannozzi%40uniud.it%7C80a986d45d644f992b5b08daa8239aab%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638007168127678002%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QNjOmuGNFazveukZ1%2BPZ7J0mlxGHxbDqpwywZMRzah0%3D&reserved=0
> 

-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


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Re: [QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Thank you Paolo. I have just a small follow up question. Is ensemble_DFT 
suitable only for cluster inside vacuum in a box, or slab inside vacuum in a 
box? 
Or, with very careful choice of inputs we can apply ensemble_DFT for 3D cases 
too? For example; if I want to simulate a Cu supercell at 300 K?

Regards,
Krishnendu


- Original Message -
From: "paolo giannozzi" 
To: users@lists.quantum-espresso.org, "KRISHNENDU MUKHERJEE" 

Sent: Friday, October 7, 2022 2:14:38 AM
Subject: Re: [QE-users] Ensemble_DFT simulation

Thank you for reporting this. Some examples have been run years ago and 
things have changed meanwhile

Paolo

On 06/10/2022 08:30, KRISHNENDU MUKHERJEE wrote:
> 
> Dear Community,
> 
> Few days back I wrote to this forum regarding the zero values of the 
> eigenvalues:
> 
> --
> 
> When I practised the example 08 given in CPV/examples, I got the note:
> 
> NOTE : eigenvalues are not computed without ortho
> 
> And the reported eigenvalues are all zeros.
> 
> However, in the given reference output the note is not there. Also, the 
> eigen values are non-zero.
> 
> Please suggest to solve the problem.
> 
> ---
> 
> To solve it, I think, one may do few steps of orthogonalization = 
> 'Gram-Schmidt', and then using the autopilot mode change it to 
> "orthogonalization = 'ortho'.
> 
> By doing so, on_step 6, I got the values of the eigenvalues.
> 
> In the reference example08, the eigenvalues at the end of step 5 were:
> 
> Eigenvalues (eV), kp =1 , spin =1
> 
> -9.73-8.12-3.55-2.45-2.45-1.20-1.200.82
> 
> After Autopilot on_step 6, to orthogonalization = ‘ortho’, at the end of 
> 10 step the eigenvalues I got is:
> 
> STEP:100.00
> 
> Eigenvalues (eV), kp =1 , spin =1
> 
> -9.75-8.13-3.56-2.46-2.46-1.21-1.210.93
> 
> I hope in this way the cp.x runs with correct eigenvalues as compared to 
> what might be happening with orthogonalization = 'Gram-Schmidt',only.
> 
> Thanking you,
> 
> Regards,
> 
> Krishnendu
> 
> 
> 
> 
> 
> ___
> 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@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


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[QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Dear Community, 



Few days back I wrote to this forum regarding the zero values of the 
eigenvalues: 

-- 

When I practised the example 08 given in CPV/examples, I got the note: 

NOTE : eigenvalues are not computed without ortho 

And the reported eigenvalues are all zeros. 

However, in the given reference output the note is not there. Also, the eigen 
values are non-zero. 

Please suggest to solve the problem. 

--- 

To solve it, I think, one may do few steps of orthogonalization = 
'Gram-Schmidt', and then using the autopilot mode change it to 
"orthogonalization = 'ortho'. 

By doing so, on_step 6, I got the values of the eigenvalues. 



In the reference example08, the eigenvalues at the end of step 5 were: 



Eigenvalues (eV), kp = 1 , spin = 1 



-9.73 -8.12 -3.55 -2.45 -2.45 -1.20 -1.20 0.82 



After Autopilot on_step 6, to orthogonalization = ‘ortho’, at the end of 10 
step the eigenvalues I got is: 



STEP: 10 0.00 

Eigenvalues (eV), kp = 1 , spin = 1 

-9.75 -8.13 -3.56 -2.46 -2.46 -1.21 -1.21 0.93 


I hope in this way the cp.x runs with correct eigenvalues as compared to what 
might be happening with orthogonalization = 'Gram-Schmidt', only. 




Thanking you, 

Regards, 

Krishnendu 


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[QE-users] Best way to choose dt and nstep in AIMD/CPMD simulation using cp.x code in quantum espresso

[KRISHNENDU MUKHERJEE]

Dear Jayraj Anadani, 

Thank you for your reply. As far as I have understood there are several ways to 
keep the electron wave functions close to the Born-Oppenheimer surface. One of 
them is as you are doing by, electron dynamics = "cg". Another one is the 
ensemble-DFT approach. I have put my questions for the ensemble-DFT approach 
under the topic, Ensemble_DFT simulation. Ensemble-DFT also does 
cg-minimization of electron wavefunctions (in an outer loop) in combination 
with updating the electron occupancy (in an inner loop). As you I am also 
trying to optimize the atomic structure of a cluster placed inside vacuum in a 
box. My computational facility is limited. So, till now I have only been able 
to simulate till 0.1 ps. So far the change in atomic structure from the input 
perfect crystal-fragment is reasonable. 

However I am getting a note, 

NOTE : eigenvalues are not computed without ortho 
And the reported eigenvalues are all zeros 

I am concerned with this NOTE as, I think the eigen values are required to 
calculate the smearing of the electrons. 

So, today my question to you is the following. Did you get this NOTE too? 

Thank you, 
Best regards, 
Krishnendu 


---you
 wrote: 

It is a cluster inside a 20 A box to remove periodicity. But that cluster 
is a part of large MD simulated position coordinates file of 1 atoms. 

Thank you 
Regards 
Jayraj Anadani 

On Sun, 2 Oct, 2022, 10:15 am KRISHNENDU MUKHERJEE,  
wrote: 

> 
> Dear Dr. Jayraj Anadani, 
> 
> Is your input atomic structure is a cluster inside vacuum in a box or it 
> is a supercell? 
> 
> Thank you, 
> Regards, 
> Krishnendu 
> 
> 
> -
>  
> You wrote: 
> In my case, I have a system of 54 zrcu atoms. i want to melt it at higher 
> temperatures above 2000K and then i will do quenching to get amorphorse 
> metallic alloys state. 
> But shorter time step in cg method give more time consuming. So i choose dt 
> = between 30 to 60 and in order to get equilibrium at high temperatures i 
> took nstep = above 500. 
> For equilibrium i have to run continue till 3 to 5 ps to get randomisation 
> so it took large time to complete. 
> Any suggestions ? 
> 
> Thank you 
> Jayraj Anadani 


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[QE-users] Best way to choose dt and nstep in AIMD/CPMD simulation using cp.x code in quantum espresso

[KRISHNENDU MUKHERJEE]

Dear Dr. Jayraj Anadani, 

Is your input atomic structure is a cluster inside vacuum in a box or it is a 
supercell? 

Thank you, 
Regards, 
Krishnendu 
-
 
You wrote: 
In my case, I have a system of 54 zrcu atoms. i want to melt it at higher
temperatures above 2000K and then i will do quenching to get amorphorse
metallic alloys state.
But shorter time step in cg method give more time consuming. So i choose dt
= between 30 to 60 and in order to get equilibrium at high temperatures i
took nstep = above 500.
For equilibrium i have to run continue till 3 to 5 ps to get randomisation
so it took large time to complete.
Any suggestions ? 
Thank you
Jayraj Anadani 

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[QE-users] FCC unit cell not identified as ibrav = 2

[KRISHNENDU MUKHERJEE]

Dear community, 

When I input the unit cell of FCC (8 corner atoms and 6 face-centered atoms), 
Quantum Espresso does not recognize it as FCC ( ibrav = 2). 

Kindly suggest. 

Regards, 
Krishnendu Mukherjee 

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[QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Dear expert, 




When I practised the example 08 given in CPV/examples, I got the note: 

NOTE : eigenvalues are not computed without ortho 

And the reported eigenvalues are all zeros. 




However, in the given reference output the note is not there. Also, the eigen 
values are non-zero. 



Please suggest to solve the problem. 



Thank you, 

Best regards, Krishnendu 


___
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[QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Dear expert, 

I determined the lattice constant of Cu from pw.x calculations. Further, 
considering the thermal expansion co-efficient of Cu I determined the lattice 
constant at 300K. However, when I did ensemble_DFT simulation of the structure 
at 300K the pressure is above 600 GPa. Can you please let me know why is the 
pressure so high? Even if the lattice constant is off by, for example, +/- 0.1 
Angstrom, the pressure should not be that high, isn’t it? Is it due to the way 
the emass_cutoff is preconditioned, that we are noticing this high pressure? 

Regards, 
Krishnendu 




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[QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Hello, 

Is it not possible to do ensemble_DFT simulation in variable cell (vc) mode? 
This is because when I set tempw = 900.D0, the cell volume should increase than 
what I did input as cell volume at ground state. This can cause the temperature 
fluctuation as I have reported before. 

Regards, 
Krishnendu 


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[QE-users] Ensemble_DFT simulation

[KRISHNENDU MUKHERJEE]

Hello, 




Kindly let me know the meaning of the outputs tempp or Tion(K). 

I set tempw = 900.D0, but these outputs were fluctuating and went as high to 
2.668054E+03. Should I run the calculations till the Tion(K) stabilizes at 900 
K? 



Regards, 

Krishnendu 

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Re: [QE-users] CP example 08

[KRISHNENDU MUKHERJEE]

Hello,

 In continuation to my earlier e-mail here is the final *.evp output:

#   nfitime(ps)ekincT_cell(K) Tion(K)  etot 
  enthal   econs   econt  Volume
Pressure(GPa)EXX   EVDW
  5  1.511803E-02  0.00E+00  0.00E+00  2.408190E+02   
-797.15162372  0.   -797.13224272   -797.13262893  
3.031904E+05  -0.0
 10  3.023605E-02  0.00E+00  0.00E+00  1.104012E+03   
-797.19457847  0.   -797.12612075   -797.13259855  
3.031904E+05  -0.0

And in the *.out file:
Averaged Physical Quantities
  accumulated  this run
   ekinc :0.0   0.0 (AU)
   ekin  :  130.25771 130.25771 (AU)
   epot  :-1065.43490   -1065.43490 (AU)
   total energy  : -797.16026-797.16026 (AU)
   temperature   :  403.06226 403.06226 (K )
   enthalpy  :0.0   0.0 (AU)
   econs : -797.13092-797.13092 (AU)
   pressure  :0.0   0.0 (Gpa)
   volume:   303190.38326  303190.38326 (AU)


Kindly let me know if further information is required to check the 
appropriateness of the input parameters,

Thank you,
Regards,
Krishnendu


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Re: [QE-users] CP example 08

[KRISHNENDU MUKHERJEE]

Hello,

 I made a modified script to study the positions of 13 copper atoms cluster at 
900 K. The initial 13 Cu atoms are cut from a regular FCC crystal.

&CONTROL
calculation = 'cp',
  restart_mode = 'from_scratch',
  nstep  = 10,
  iprint = 5,
  isave  = 5,
  dt= 125.0d0,
  prefix = 'Cu_cluster',
  pseudo_dir = '/scratch/krishnen/qe-6.4/q-e-qe-6.4/pseudo/',
  outdir='/scratch/krishnen/qe-6.4/q-e-qe-6.4/tempdir/'
  ndr=50
 ndw=51
/
&SYSTEM
 ibrav = 0,
  nat  =13,
  ntyp =1,
  nspin=1,
  ecutwfc = 47.0,
  ecutrho = 376.0,
   nbnd=120,
 input_dft = 'pbe'
  occupations = 'ensemble',
  smearing='cs',
  degauss=0.018,
  nr1b=24,nr2b=24,nr3b=24
/
&ELECTRONS
 orthogonalization = 'Gram-Schmidt',
  startingwfc = 'random',
  ampre = 0.02,
  tcg = .true.,
   passop=0.3,
  maxiter = 250,
 emass_cutoff = 3.0d0,
  conv_thr=1.d-6
  n_inner = 2,
  lambda_cold = 0.03,
  niter_cold_restart = 2,
/
&IONS
 ion_dynamics = 'verlet',
  ion_temperature = 'nose',
fnosep = 4.0d0,
  tempw = 900.D0,
/
ATOMIC_SPECIES
Cu   63.55  Cu.pbe-dn-rrkjus_psl.1.0.0.UPF
CELL_PARAMETERS angstrom
 35.55000.0.
  0.   35.55000.
  0.0.   35.5500
ATOMIC_POSITIONS angstrom
Cu   15.8000   17.7750   13.8250
Cu   17.7750   15.8000   13.8250
Cu   19.7500   17.7750   13.8250
Cu   17.7750   19.7500   13.8250
Cu   15.8000   15.8000   15.8000
Cu   17.7750   17.7750   15.8000
Cu   15.8000   17.7750   17.7750
Cu   17.7750   15.8000   17.7750
Cu   19.7500   15.8000   15.8000
Cu   19.7500   17.7750   17.7750
Cu   15.8000   19.7500   15.8000
Cu   17.7750   19.7500   17.7750
Cu   19.7500   19.7500   15.8000
---
At the step 5 the *.evp file gave the following:

#   nfitime(ps)ekincT_cell(K) Tion(K)  etot 
  enthal   econs   econt  Volume
Pressure(GPa)EXX   EVDW
  5  1.511803E-02  0.00E+00  0.00E+00  2.408190E+02   
-797.15162372  0.   -797.13224272   -797.13262893  
3.031904E+05  -0.0

Kindly let me know if the input values for the script are correct? I will once 
again update the results when all the 10 nsteps are complete. 

Thank you,
Regards,
Krishnendu


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Re: [QE-users] CP example 08

[KRISHNENDU MUKHERJEE]

Hello,

 I made the following script to see the evolution of a 43 copper atoms cluster 
at 900 K.

&CONTROL
  calculation = 'cp',
  restart_mode = 'from_scratch',
  verbosity = 'high',
  nstep  = 5,
  iprint = 10,
  isave  = 1000,
  tstress = .TRUE.,
  tprnfor = .TRUE.,
  dt= 20.0d0,
  prefix = 'Si_dimer',
  pseudo_dir = '/home/krishnendu/backupable/qe/q-e-qe-6.5/pseudo/',
  outdir='/home/krishnendu/backupable/qe/q-e-qe-6.5/tempdir/'

/

&SYSTEM
  ibrav = 0,

!  nbnd=10,
  
  nat  =43,
  ntyp =1,
  ecutwfc = 47.0,
  ecutrho = 376.0,
  nr1b=20,nr2b=20,nr3b=20
  occupations = 'ensemble',
  smearing='fd',
  degauss=0.025,
  nspin=1,
/

&ELECTRONS
  emass = 300.d0,
  emass_cutoff = 2.5d0,
  orthogonalization = 'Gram-Schmidt',
  startingwfc = 'random',
  ampre = 0.02,
  n_inner = 8,
  tcg = .true.,
  passop=0.3,
  maxiter = 250,
  conv_thr=1.d-6
/

&IONS
  ion_dynamics = 'verlet',
  ion_velocities= 'random',
!  ion_temperature = 'nose',
  tempw = 900.D0,
!  tolp = 100.D0, 
/

ATOMIC_SPECIES
Cu   63.55  Cu.pbe-dn-rrkjus_psl.1.0.0.UPF


CELL_PARAMETERS angstrom
 35.55000.0.
  0.   35.55000.
  0.0.   35.5500
 
ATOMIC_POSITIONS angstrom
Cu   15.8000   13.8250   13.8250
Cu   19.7500   13.8250   13.8250
Cu   13.8250   15.8000   13.8250
Cu   15.8000   15.8000   11.8500
Cu   17.7750   17.7750   11.8500
Cu   15.8000   17.7750   13.8250
Cu   17.7750   15.8000   13.8250
Cu   19.7500   15.8000   11.8500
Cu   19.7500   17.7750   13.8250
Cu   21.7250   15.8000   13.8250
Cu   13.8250   19.7500   13.8250
Cu   15.8000   19.7500   11.8500
Cu   15.8000   21.7250   13.8250
Cu   17.7750   19.7500   13.8250
Cu   19.7500   19.7500   11.8500
Cu   19.7500   21.7250   13.8250
Cu   21.7250   19.7500   13.8250
Cu   17.7750   13.8250   15.8000
Cu   15.8000   13.8250   17.7750
Cu   19.7500   13.8250   17.7750
Cu   13.8250   17.7750   15.8000
Cu   13.8250   15.8000   17.7750
Cu   15.8000   15.8000   15.8000
Cu   17.7750   17.7750   15.8000
Cu   15.8000   17.7750   17.7750
Cu   17.7750   15.8000   17.7750
Cu   19.7500   15.8000   15.8000
Cu   21.7250   17.7750   15.8000
Cu   19.7500   17.7750   17.7750
Cu   21.7250   15.8000   17.7750
Cu   13.8250   19.7500   17.7750
Cu   15.8000   19.7500   15.8000
Cu   17.7750   21.7250   15.8000
Cu   15.8000   21.7250   17.7750
Cu   17.7750   19.7500   17.7750
Cu   19.7500   19.7500   15.8000
Cu   19.7500   21.7250   17.7750
Cu   21.7250   19.7500   17.7750
Cu   15.8000   15.8000   19.7500
Cu   17.7750   17.7750   19.7500
Cu   19.7500   15.8000   19.7500
Cu   15.8000   19.7500   19.7500
Cu   19.7500   19.7500   19.7500


I got the following error:

YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

Kindly suggest.

Thank you Pietro for replying my earlier question.

Regards,
Krishnendu

--

Message: 15
Date: Fri, 12 Aug 2022 08:34:53 +
From: Pietro Davide Delugas 
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] R: CP example 08
Message-ID:



Content-Type: text/plain; charset="utf-8"

Hello,
CP works using orbitals computed at the zone center of your supercell's 
reciprocal lattice, so no need to specify k-points.
It's like when using pw you specify

K_POINTS gamma

?best regards - Pietro

Da: users  per conto di KRISHNENDU 
MUKHERJEE 
Inviato: venerd? 12 agosto 2022 09:50
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] CP example 08


Dear Expert,

 In the CP package in example 08, why there are no k-points given?

Regards,
Krishnendu





__

[QE-users] CP example 08

[KRISHNENDU MUKHERJEE]

Dear Expert, 

In the CP package in example 08, why there are no k-points given? 

Regards, 
Krishnendu 

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Re: [QE-users] How to input SQS

[Krishnendu Mukherjee]

Dear Dr. Sunil Kumar,

 Thank you for your reply. The SQS was built for a 4-atom equimolar HEA.
For, example the atoms are: Ni, Fe, Cr and Co.

Thanking you,
Regards,
Krishnendu


> Message: 8
> Date: Wed, 26 Aug 2020 22:41:52 +0530
> From: "Dr. SUNIL KUMAR" 
> To: Quantum ESPRESSO users Forum 
> Subject: Re: [QE-users] How to input SQS
> Message-ID:
> <
> cade9o7k5pgfkoqrvktmu9b18aw8ik0vpw-9utnuuww3z_ag...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> What is the name of metal atoms of HEA?
>
> Thanks
> With regards
> SUNIL
> Dr. Sunil Kumar
> Ph.D (Chemical Engg. IIT Delhi)
> M.Tech (Chemical Engg. IIT Delhi)
> B.Tech (Chemical Engg. IET-CSJMU Kanpur)
> Scientist-C
> CSIR-National Metallurgical Laboratory Jamshedpur-831007
> http://www.nmlindia.org/
> https://scholar.google.co.in/citations?user=OchYqugJ&hl=en&oi=sra
>
>
>
> On Wed, Aug 26, 2020 at 4:57 PM Krishnendu Mukherjee <
> krishnendu.mukherjee...@gmail.com> wrote:
>
>
>  Dear Expert,
>
>  I want to perform a 'scf' calculation for a Quasi Random Structure (SQS).
>  It is FCC. In the book chapter titled, "Applications of Special
>  Quasi-random Structures to High-Entropy Alloys", by Michael C. Gao,
>  Changning Niu, Chao Jiang, and Douglas L. Irving, the lattice vectors are
>  given as
>
>  0.5 - 0.5 -1
>  -1.5 -1.5 0.0
>  -1.5 1.5 -1.0
>
>  The atomic positions for the 24 atoms are given in fractional co-ordinates
>  for the unrelaxed lattice.
>  [Reference:  Gao M.C., Niu C., Jiang C., Irving D.L. (2016) Applications
>  of Special Quasi-random Structures to High-Entropy Alloys. In: Gao M., Yeh
>  JW., Liaw P., Zhang Y. (eds) High-Entropy Alloys. Springer, Cham.
> https://doi.org/10.1007/978-3-319-27013-5_10  ]
>
>  Can you kindly guide me how to input this structure into Quantum Espresso
>  for 'scf' calculation?
>
>  Thanking you,
>  Best regards,
>  Krishnendu
>
>  --
>  Dr. Krishnendu Mukherjee,
>
>  Principal Scientist,
>  CSIR-NML,
>  Jamshedpur.
>  ___
>
>
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[QE-users] How to input SQS

[Krishnendu Mukherjee]

Dear Expert,

I want to perform a 'scf' calculation for a Quasi Random Structure (SQS).
It is FCC. In the book chapter titled, "Applications of Special
Quasi-random Structures to High-Entropy Alloys", by Michael C. Gao,
Changning Niu, Chao Jiang, and Douglas L. Irving, the lattice vectors are
given as

0.5 - 0.5 -1
-1.5 -1.5 0.0
-1.5 1.5 -1.0

The atomic positions for the 24 atoms are given in fractional co-ordinates
for the unrelaxed lattice.
[Reference:  Gao M.C., Niu C., Jiang C., Irving D.L. (2016) Applications of
Special Quasi-random Structures to High-Entropy Alloys. In: Gao M., Yeh
JW., Liaw P., Zhang Y. (eds) High-Entropy Alloys. Springer, Cham.
https://doi.org/10.1007/978-3-319-27013-5_10  ]

Can you kindly guide me how to input this structure into Quantum Espresso
for 'scf' calculation?

Thanking you,
Best regards,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Symmetry operation identification for supercell

[Krishnendu Mukherjee]

  ( -0.866 -0.500  0.000 )
  (  0.000  0.000  1.000 )


 point group D_3d (-3m)
 there are  6 classes
 the character table:

   E 2C3   3C2'  i 2S6   3s_d
A_1g   1.00  1.00  1.00  1.00  1.00  1.00
A_2g   1.00  1.00 -1.00  1.00  1.00 -1.00
E_g2.00 -1.00  0.00  2.00 -1.00  0.00
A_1u   1.00  1.00  1.00 -1.00 -1.00 -1.00
A_2u   1.00  1.00 -1.00 -1.00 -1.00  1.00
E_u2.00 -1.00  0.00 -2.00  1.00  0.00

 the symmetry operations in each class and the name of the first
element:

 E1
  identity
 2C3  34
  120 deg rotation - cryst. axis [0,0,1]
 3C2' 256
  180 deg rotation - cart. axis [1,0,0]
 i7
  inversion
 2S6  9   10
  inv. 120 deg rotation - cryst. axis [0,0,1]
 3s_d 8   11   12
  inv. 180 deg rotation - cart. axis [1,0,0]

 Space group identification,  12 symmetries:

 Bravais lattice   4  hexagonal
 Point group number  25 / 118  D_3d (-3m)

 Nonsymmorphic operations not found: All fractional translations vanish
 Symmetries of the point group in standard order

1   E   1
2  3z  27
3 3-z  28
4  2x   4
52110  32
62010  31
7   i  33
8 i3z  59
9i3-z  60
   10 i2x  36
   11   i2110  64
   12   i2010  63


 Space group nymber  164

 Space group P-3m1   (group number 164).
 The origin coincides with the ITA tables.

 The Laue class is D_3d (-3m)

 In this class the elastic tensor is

 ( c11  c12  c13  c14   ..  )
 ( c12  c11  c13 -c14   ..  )
 ( c13  c13  c33   ...  )
 ( c14 -c14   .   c44   ..  )
 (  ....   c44  c14 )
 (  ....   c14   X  )
 X=(c11-c12)/2

 It requires three strains: e1, e3, and e4
 for a total of 12 scf calculations

 --
 Ions are relaxed in each calculation
 ------



Thanks,
Best regards,
Krishnendu


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Zr supercell

[Krishnendu Mukherjee]

Dear Dr. Mostafa Youssef,

 Thank you very much for your kind reply. I am trying to build a supercell.
I got another reply in this forum that there has to be at least two Nb
atoms as there is no Wyckofff positions having only 1 atom in the space
group 194. If I want to use the Wyckoff positions I have to use the ones
having no x, y, z parameters in them, because at present I have no
crystallographic information about the Zr-Nb alloy. I may assume that Zr
atoms are in the Wyckoff positions, 2b, 2c, 2d and 6g positions (=total 12
Zr atoms) and Nb atoms are in 2a positions (=2 atoms). These are also
assumptions but at present I do not have any other options to start with.
Of course I suppose this will keep the space group intact, i.e., if I put
the atoms in these Wyckoff positions quantum espresso will be able to
determine the space group as 194.

 Please let me know your comments and suggestions regarding building up the
supercell.
Thanking you,
Yours sincerely,
Krishnendu
---

You wrote:

Dear Krishnendu,

If you model the alloy using a unit cell, then you are modeling a very high
Nb concentration ordered alloy.

Take HCP unit cell having two Zr atoms. If you replace one with Nb, then
you get 50%-50% Zr-Nb.

There is no way to avoid forming a supercell of Zr (Say 54 atoms) and then
replace one with Nb.


Regards,
AUC, New Cairo, Egypt

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Problem regarding identification of space group of Zr15Nb1 cell

[Krishnendu Mukherjee]

Respected Dr. M. Mehl,

 Thank you very much for your kind reply.




It's impossible for space group #194 to have 15 atoms of one species and 1
atom of another species -- there aren't any Wyckoff positions in P6_3/mmc
that contain only one point.

What you've done eliminates the inversion operation, which changes #194 to
#187.

Take a look at both space groups in the International Tables or
http://www.cryst.ehu.es/cryst/get_wp.html and you'll see this.

On Fri, Feb 9, 2018 at 4:48 AM, Krishnendu Mukherjee <
krishnendu.mukherjee...@gmail.com> wrote:

>
> Dear Experts,
>
>  I have created a Zr15Nb1 cell containing 15 Zr atoms and 1 Nb atom using
> the space group P 63/m m c, (space group number 194).
>
>  But, when I try to calculate the elastic constant of it using the
> thermo_pw, I find, pwscf recognizes wrong space group (No. 187). Please
> find below my input:

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Problem regarding identification of space group of Zr15Nb1 cell

[Krishnendu Mukherjee]

tal of 12 scf calculations

*********

It will be great if you can help me in solving this problem,

Thanks,
Best regards,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Zr supercell

[Krishnendu Mukherjee]

Dear expert,

 This is in response to the question why do we want to use a Zr supercell.
We are interested in calculating the elastic constants of Zr alloys (for
example Zr containing 1 wt% Nb). We found a paper titled, "Mechanical
properties of zirconium alloys and zirconium hydrides predicted from
density functional perturbation theory". In that paper the authors
constructed a Zr53Nb supercell with 53 Zr atoms and 1 Nb atom to do the
calculations. As a first step we want to replicate the results. To begin,
we just try to make a Zr supercell. When we are successful in creation of
Zr supercell and able to predict the elastic constants of Zr with the
supercell properly we will replace a Zr atom in that supercell with Nb to
get the elastic constants of the alloy.

 Now my question is,  is it possible to calculate the elastic properties of
Zirconium alloy without constructing a supercell, i.e., through an unit
cell? In that can you please let us know what will be the input parameters
to construct such an unit cell?

 Now in case, if construction of supercell is unavoidable can you please
guide us what are the input to construct the supercell. I guess we have to
input the space group (194, P 63/m m c in this case). I guess the other
input is the basis atom positions which is 0,0,0 and 2/3, 1/3, 1/2. Is
there any other input for constructing a supercell. I will use the program
VESTA for creating a supercell.

 I found some previous discussions in the pwscf forum about the space group
194. There I saw ibarv=4 was used, with some other necessary inputs,
e.g., use_all_frac = .true.. But in that case the input for the
ATOMIC_POSITIONS are to be given in crystal_sg. But I do not know how to
get the crystal_sg output from VESTA.

 I will be grateful to you if you can kindly guide us regarding these
matters.

Thanking you,
Yours sincerely,
krish


-- 
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Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Zr supercell with ibrav=4

[Krishnendu Mukherjee]

Dear experts,

 I am interested in calculation of elastic constants of Zr using a
supercell of 2*2*2. I created this supercell in VESTA, using Space group
No. 194, P 63/m m c. For the unit cell structure Parameters I used:

0.33 0.67 0.25
and
0.67 0.33 0.75

I have input the atomic positions into the following input:

&control
calculation = 'scf'
restart_mode='from_scratch',
prefix='zr',
tstress = .true.,
   tprnfor = .true.,
pseudo_dir = '/home/krishna/QE/qe-6.2/pseudo/',
outdir='/home/krishna/QE/qe-6.2/tempdir/'
 /
 &system
ibrav=  4,
celldm(1) =12.241645,
celldm(3) = 1.59185,
nat= 16,
ntyp= 1,
ecutwfc=50.0,
   ecutrho = 430,
   occupations='smearing',
   smearing='marzari-vanderbilt',
   degauss=0.02
   starting_magnetization(1) = 0.7,
 /
 &electrons
conv_thr =  1.0d-12
 /
ATOMIC_SPECIES
 Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Zr0.001.8700381.289000
Zr3.2390003.7400759.023001
Zr1.6195004.6750941.289000
Zr1.6195000.9350199.023001
Zr   -1.6195004.6750941.289000
Zr4.8585000.9350199.023001
Zr3.2390003.7400753.867000
Zr1.6195000.9350193.867000
Zr4.8585000.9350193.867000
Zr0.001.8700386.445000
Zr1.6195004.6750946.445000
Zr   -1.6195004.6750946.445000
Zr3.2390001.8700381.289000
Zr0.003.7400759.023001
Zr0.003.7400753.867000
Zr3.2390001.8700386.445000
K_POINTS AUTOMATIC
5 5 3 0 0 0

However, in out.1_0, in notice that

Space group nymber  164

Is it an error, because I generated the supercell using space group number
194?

 If it is an error can you please let me know, how to modify the input?

However, when I ran the program with an unit cell of two atoms the space
group number was rightly identified as 194.

Thanks,
Best regards,
Krish

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Zr supercell with ibrav=0

[Krishnendu Mukherjee]

Dear experts,

 I am interested in calculation of elastic constants of Zr using a
supercell of 2*2*2. I have used ibrav=0. I used the following input:


cat > thermo_control << EOF
 &INPUT_THERMO
  what='mur_lc_elastic_constants',
  frozen_ions=.FALSE.
 /
EOF

cat > zr.elastic.in << EOF
 &control
calculation = 'scf'
restart_mode='from_scratch',
prefix='zr',
tstress = .true.,
   tprnfor = .true.,
pseudo_dir = '$PSEUDO_DIR/',
outdir='$TMP_DIR/'
 /
 &system
ibrav= 0,
nat= 16,
ntyp= 1,
ecutwfc=50.0,
   ecutrho = 430,
   occupations='smearing',
   smearing='marzari-vanderbilt',
   degauss=0.02
   starting_magnetization(1) = 0.7,
 /
 &electrons
conv_thr =  1.0d-12
  /
ATOMIC_SPECIES
 Zr  91.22  Zr.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Zr 0.00 1.870038 1.289000
Zr 3.239000 3.740075 9.023001
Zr 1.619500 4.675094 1.289000
Zr 1.619500 0.935019 9.023001
Zr -1.619500 4.675094 1.289000
Zr 4.858500 0.935019 9.023001
Zr 3.239000 3.740075 3.867000
Zr 1.619500 0.935019 3.867000
Zr 4.858500 0.935019 3.867000
Zr 0.00 1.870038 6.445000
Zr 1.619500 4.675094 6.445000
Zr -1.619500 4.675094 6.445000
Zr 3.239000 1.870038 1.289000
Zr 0.00 3.740075 9.023001
Zr 0.00 3.740075 3.867000
Zr 3.239000 1.870038 6.445000
/
CELL_PARAMETERS (ANGSTROM)
6.4780001640 0.00 0.00
-3.239820 5.6101127078 0.00
0.00 0.00 10.3120002747
/
K_POINTS AUTOMATIC
5 5 3 0 0 0
EOF

Can you kindly let me know why I am getting the following error:

from card_atomic_positions : error # 2
     two occurrences

I will be grateful if you can help me in solving the problem.

Thanks,
Regards,
krish
-- 
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Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Units for celldm(1)

[Krishnendu Mukherjee]

 Dear experts,

 I have developed a 3*3*3 supercell for Zr using Vesta. I find the units of
the XYZ positions of Zr is in Angstrom.

 In that case, for the pw.x input what should be the unit of celldm(1)?

Thanks,
Best regards,
Krishnendu


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CSIR-NML,
Jamshedpur.
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[Pw_forum] nspin values

[Krishnendu Mukherjee]

Dear Dr. Daniele,

 Thank you very much for your detailed reply to my question regarding
Fourier interpolation for DFPT.

 I am trying to replicate the results of your article, "Thermoelastic
properties of alpha-iron from first-principles" published in PRB 91,
104105, in 2015.

 I used the pseudo potential Fe.pbe-spn-rrkjus psl.0.2.1.UPF, and other
values of parameter (e.g. wavefunction kinetic-energy cut off of 90 Ry
etc.) as mentioned in the first two paragraphs of the section : III.
COMPUTATIONAL DETAILS AND PSEUDOPOTENTIAL SELECTION.

I have coupled thermo_pw.0.8.0 with QE-6.2. The script file I used is:

cat > thermo_control << EOF
 &INPUT_THERMO
  what='scf_disp',
  nq1_d=128,
  nq2_d=128,
  nq3_d=128,
 /
EOF
cat > fe.scf_disp.in << EOF
 &control
   calculation = 'scf'
   prefix='fe',
   pseudo_dir = '$PSEUDO_DIR/',
   outdir='$TMP_DIR/'
 /
 &system

ibrav = 3, celldm(1) =5.217, nat= 1, ntyp= 1,
ecutwfc = 90.0,ecutrho = 1080.0,
 occupations='smearing', smearing='marzari-vanderbilt', degauss=0.005
nspin = 2
starting_magnetization(1) = 0.5
/
 &electrons
conv_thr = 1.0e-16,
 mixing_beta = 0.2
 /
ATOMIC_SPECIES
 Fe 55.847 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
ATOMIC_POSITIONS (alat)
 Fe 0.0 0.0 0.0
K_POINTS {automatic}
 24 24 24 1 1 1
EOF
cat > ph_control << EOF

 &inputph
  tr2_ph = 1.0e-16,
  prefix='fe',
  fildyn='fe.dyn',
  ldisp=.TRUE.
  nq1=4, nq2=4, nq3=4,

/
EOF

With the above input the generated fe.dyn.g1.1 dynamic matrix has negative
values of frequencies.

 I guess I am not using the correct value of nspin. as according to pw.x
input description, nspin = 2, is for:

 spin-polarized calculation, LSDA
  (manetization along z axis)

However, for the GGA functional (Fe.pbe-spn-rrkjus_psl.0.2.1.UPF) I do not
know what is the value of nspin I should be using.

So, my question is kindly let me know the value of nspin I should use.
Also, if possible, please let me know if any other parameters I have input
has incorrect values or needs improvement.

Thanking you,
Best regards,
Krishnendu



--

Date: Fri, 5 Jan 2018 13:42:57 +
From: Dragoni Daniele 
Subject: Re: [Pw_forum] Fourier interpolation for DFPT
To: PWSCF Forum 
Message-ID: <1515159777313.75...@epfl.ch>
Content-Type: text/plain; charset="iso-8859-1"

Dear Krishnendu,


in order to perform the so-called Fourier-interpolation you need first to
compute phonon frequencies with DPTF on a proper grid of q-points using
ph.x. From the dynamical matrix produced by the phonon code you can then
compute the interatomic force constants (IFC) in real space using the q2r.x
code. From there, it is possible to recompute the phonon frequencies at any
arbitrary q-point by means of the matdyn.x code. At this stage, you can
specify the q-mesh (or a list of specific q-points) that is required for
calculating converged values of the quantities you are interested in (in
our case a 21x21x21 mesh was sufficient). For more specific information,
try to have a look at this very useful document by Paolo Giannozzi
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_disp.html


Both q2r.x and matdyn.x should be automatically compiled by typing "make
ph" from the main quantum Espresso directory, as stated (for example) here
http://www.afs.enea.it/software/qu_esp/Doc/ph_6.0.0.pdf


Examples of q2r and matdyn input files can be found here

http://www.fisica.uniud.it/~giannozz/QE-Tutorial/examples_disp.tgz

Have also a look at this tutorial (Exercise 2 in particular)

http://www.tcl.t.u-tokyo.ac.jp/pdf/2014_lm/3rd_day_pm.pdf


In particular you can read:

##q2r input template

&INPUT
fildyn = ***,
flfrc  = ***,
zasr   = ***,(we use crystal)
 /

##


## matdyn input template

&INPUT
ntyp  = ***,(we have 1 atom type)
flvec = ***,
flfrc = ***,
asr   = ***,(we use crystal)
amass(1) = ***,
/
***   (integer # of q points for which you want compute phonon
frequencies)
x1 x2 x3  0 (here goes a list of q points coordinates followed by a growing
integer number N counting the q-points. In our case, this list should
correspond to a 21x21x21 MP grid)

x1 x2 x3  1
x1 x2 x3  2

...

...

##

Replace *** with the correct input card. An exhaustive description of the
input cards available for the two codes can be found in the header of the
source codes q2r.f90 and matdyn.f90 in /yourQEfolder/PHonon/PH directory.


Hope this helps!

Best regards,

   Daniele

__

Daniele Francesco Dragoni
Laboratoire de th?orie et simulation des mat?riaux
Swiss Federal Institute of Technology
EPFL STI IMX THEOS
ME D2 1020
Station 9
CH-1015, Lausanne
+41 21 69 31956



F

[Pw_forum] Phonon calculation for Zr

[Krishnendu Mukherjee]

Dear Experts,

 I am interested in phonon calculation for Zr. I found the following useful
post in the QE-forum (please see below).

 Can you please let me know where to put the values for nr1, nr2 and nr3. I
mean is it to be put in scf.in, ph.in or q2r.in?

 And also if possible please let me know what does nr represents?

Thanking you,
Yours sincerely,
Krishnendu


---


[Pw_forum] Bug in ph.x sometimes occur in hexagonal phases *Uri
Argaman* argamanu
at post.bgu.ac.il

*Thu Aug 27 12:56:57 CEST 2015*

   - Previous message: [Pw_forum] Bug in ph.x sometimes occur in hexagonal
   phases <http://qe-forge.org/pipermail/pw_forum/2015-August/107726.html>
   - Next message: [Pw_forum] XSpectra and US or PAW pseudos?
   <http://qe-forge.org/pipermail/pw_forum/2015-August/107732.html>
   - *Messages sorted by:* [ date ]
   <http://qe-forge.org/pipermail/pw_forum/2015-August/date.html#107729> [
   thread ]
   <http://qe-forge.org/pipermail/pw_forum/2015-August/thread.html#107729> [
   subject ]
   <http://qe-forge.org/pipermail/pw_forum/2015-August/subject.html#107729> [
   author ]
   <http://qe-forge.org/pipermail/pw_forum/2015-August/author.html#107729>

--

Thank you Andrea
I think the phonon calculated with 13 dynamical matrices is wrong because
when I calculate the anisotropic coefficients of thermal expansion in
zirconium I do PW calculations as well as phonon calculations in several
lattice parameters. In some of them (not in all of them), QE calculate 13
dynamical matrices and in the other 12. When I use this data to calculate
the anisotropic coefficient of thermal expansion I got very strange results
that do not agree with some publications which also calculate it from DFT.
I do not know what is the problem. Maybe there is some problem in q2r.x.
Using nr1=30, nr2=30, nr3=48 indeed solve the problem. In addition,
different ecut and ecutrho also solve the problem.
I now calculate the coefficient of anisotropic thermal expansion in
zirconium again with ecut=50 and ecutrho=250. These calculations always
produce 12 dynamical matrices. These calculations takes a few days on my
machines. When I will get the results I will report if it makes any
difference.
Uri Argaman
Ben-Gurion University
Israel



-- 
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Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Fourier interpolation for DFPT

[Krishnendu Mukherjee]

Dear experts,

 I am interested in calculating the phonon calculation of bcc iron ferrite.
I am following the article titled "Thermoelastic properties of alpha-iron
from first-principles" authored by Daniele Dragoni, Davide Ceresoli and
Nicola Marzari, published in PRB 91, 104105. In that article it is
mentioned that,

"Phonon calculations were carried out for each deformation within DFPT. The
dynamical matrix and its eigenvalues are calculated on an 4x4x4 mesh of
special points in the BZ and Fourier-interpolated on an extended 21x21x21
grid for integration of thermodynamic quantities."

 Now I gave the nq1=4, nq2=4, nq3=4 at fe.ph.in according to the values
mentioned in the article.

 But I do not know the parameter for which I have to set the values
21x21x21. Can you kindly let me know the parameter where I have to put the
values to set the Fourier-interpolation extension grid for integration of
thermodynamic quantities.

Thanking you,
Yours sincerely,
Krishnendu

-- 
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Principal Scientist,
CSIR-NML,
Jamshedpur.
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Re: [Pw_forum] Problem during phonon calculation of bcc iron

[Krishnendu Mukherjee]

Dear Dr. Lorenzo Paulatto,

 Thank you for your reply. While learning about the Density Functional
Perturbation Theory I am practising the phonon calculation for bcc iron
with Quantum espresso 6.2. So, I need kind help from you regarding the
meaning of different parameters.

 Your reply gave me the confidence that there was no Fortran language/ or
LINUX command related problem. As per your suggestion I started to change
different parameters to make run the code till end. First of all I
decreased the values of conv_thr to 1.0e-16 and tr2_ph to 1.0e-16.

 I realized that fe.dyn1, fe.dyn2, fe.dyn3 . are calculated one after
another. And if in one of them if freq(1,2,3) becomes too negative the
calculation stops. Please let me know if that is the case.

 Then I checked the discussions at pw_forum and found this topic was
discussed at http://qe-forge.org/pipermail/pw_forum/2014-August/104992.html
As per the discussion when I increased the ecutrho from 200.0 to 400.0 the
code ran till end, although there were negative frequencies. So, is it true
that increasing the ecutrho helps in convergence of the code?

I have another question about the parameter mixing_beta . I did calculation
with a value of 0.2. Should I increase or decrease the value to have
positive values of frequencies.

Further I changed the K_POINTS to {automatic}  8 8 8  1 1 1. In future I
plan to change it to 12 12 12 1 1 1 and to 16 16 16 1 1 1.

Thanking you,
Yours sincerely,
Krishnendu


Message: 12
Date: Tue, 26 Dec 2017 11:57:22 +0100
From: Lorenzo Paulatto 
Subject: Re: [Pw_forum] Problem during phonon calculation of bcc iron
ferrite
To: pw_forum@pwscf.org
Message-ID: <0f6d3673-f689-e709-b6d9-4e87649d5...@gmail.com>
Content-Type: text/plain; charset=utf-8; format=flowed

On 26/12/17 10:20, Krishnendu Mukherjee wrote:
> Fortran runtime error: End of file
The file fe.dyn2 is probably empty, likely because the phonon
calculation did not finish correctly.

I think you should start from scratch, paying attention to detail,
taking the necessary time to check that every step completes correctly
or understanding why it doesn't.

kind regards


--
Lorenzo Paulatto - Paris


--



-- 
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Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Problem during phonon calculation of bcc iron ferrite

[Krishnendu Mukherjee]

Dear Experts,

 Finally I am able to edit the qe-6.2-examples/PHonon/examples/example02
run_example file to calculate the fe.dispersions and fe.phdos. I have
included the edited file.

 When I changed the pseudo-potential file from Fe.pz-nd-rrkjus.UPF to
Fe.pbe-spn-rrkjus_psl.0.2.1.UPF, I got an error

transforming C(q) => C(R)...At line 116 of file io_dyn_mat_old.f90 (unit =
1, file = 'fe.dyn2')
Fortran runtime error: End of file

I have included the output of the code in the file called error.

Please help me to solve the problem,

Thanking you,
Best regards,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.


run_Fe20171222-02
Description: Binary data


error
Description: Binary data
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[Pw_forum] Example matdyn.in file for bcc iron ferrite

[Krishnendu Mukherjee]

Dear experts,

 Is it possible to have an example matdyn.in file for bcc iron ferrite. I
am interested in calculating phonon dispersion for the same as was reported
in the paper:

Dal Corso, A., and S. de Gironcoli, 2000, Phys. Rev. B 62, 273.


Thanking you,
Yours sincerely,
Krishnendu

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Principal Scientist,
CSIR-NML,
Jamshedpur.
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Re: [Pw_forum] Guidance regarding calculation of fephdos of bcc iron ferrite

[Krishnendu Mukherjee]

Dear Experts,

Please ignore my last e-mail (see attached below). I found out an error. In
the command

fildyn = 'fe.dyn',

at
# phonon calculation on a (444) uniform grid of q-points

I gave it wrongly as 'fe.dyn,

I corrected it and the program is running now doing the phonon calculation,

Sorry for the inconvenience caused,

Best regards,
Krishnendu


On Wed, Dec 6, 2017 at 12:31 PM, Krishnendu Mukherjee <
krishnendu.mukherjee...@gmail.com> wrote:

>
> Respected Experts,
>
> I wish to calculate the Vibrational free energy of bcc iron ferrite using
> the fqha.x command. For that I want to calculate fephdos.
>
>  I started modifying the qe-6.2-examples/PHonon/examples/example02. The
> examples was for AlAs. I modified it as far as I could.
>
> I got the following errors while running it:
>
> This example shows how to calculate interatomic force constants in
> real space for Fe.
>
>   executables directory: /home/krishna/QE/qe-6.2/bin
>   pseudo directory:  /home/krishna/QE/qe-6.2/pseudo
>   temporary directory:   /home/krishna/QE
>   checking that needed directories and files exist... done
>
>   running pw.x as:  /home/krishna/QE/qe-6.2/bin/pw.x
>   running ph.x as:  /home/krishna/QE/qe-6.2/bin/ph.x
>   running q2r.x as: /home/krishna/QE/qe-6.2/bin/q2r.x
>   running matdyn.x as:  /home/krishna/QE/qe-6.2/bin/matdyn.x
>   running plotband.x as: /home/krishna/QE/qe-6.2/bin/plotband.x
>   running gnuplot as: /usr/bin/gnuplot
>
>   cleaning /home/krishna/QE... done
>   running the scf calculation/run_exampleFe: line 152: check_failure:
> command not found
>  done
>   running the phonon calculation ...STOP 1
> ./run_exampleFe: line 172: check_failure: command not found
>  done
>   transforming C(q) => C(R)...At line 144 of file q2r.f90 (unit = 5, file
> = 'stdin')
> Fortran runtime error: End of file
> ./run_exampleFe: line 183: check_failure: command not found
>  done
>   recalculating omega(q) from C(R)...At line 795 of file matdyn.f90 (unit
> = 1, file = '�� ')
> Fortran runtime error: File 'fe444.fc' does not exist
> ./run_exampleFe: line 202: check_failure: command not found
>  done
>   writing the phonon dispersions in freq.plot...STOP Error reading file
> header
> ./run_exampleFe: line 216: check_failure: command not found
>  done
>   creating the postscript file fe.dispersion.ps/run_exampleFe: line
> 250: check_failure: command not found
>  done
>   calculating phonon DOS ...At line 795 of file matdyn.f90 (unit = 1, file
> = '�ݝ ')
> Fortran runtime error: File 'fe444.fc' does not exist
> ./run_exampleFe: line 264: check_failure: command not found
>  done
>   generating plot of phonon_dos in the file fe.phdos.ps..."gnuplot1.tmp",
> line 9: warning: Skipping unreadable file "fe.phdos"
> "gnuplot1.tmp", line 9: No data in plot
>
> ./run_exampleFe: line 283: check_failure: command not found
>  done
>
> /home/krishna/QE/qe-6.2-examples/PHonon/examples/example02: done
>
>
> Can you please guide me with correction of the problem. Or else if there
> is some example with phdos calculation of bcc iron ferrite please help me
> with that.
>
> I am including the modified set up so that you can possibly guide me with
> identifying the error,
>
> Thanks,
> Best regards,
> Krishnendu
>
>
> --
> Dr. Krishnendu Mukherjee,
>
> Principal Scientist,
> CSIR-NML,
> Jamshedpur.
>



-- 
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Principal Scientist,
CSIR-NML,
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[Pw_forum] Guidance regarding calculation of fephdos of bcc iron ferrite

[Krishnendu Mukherjee]

Respected Experts,

I wish to calculate the Vibrational free energy of bcc iron ferrite using
the fqha.x command. For that I want to calculate fephdos.

 I started modifying the qe-6.2-examples/PHonon/examples/example02. The
examples was for AlAs. I modified it as far as I could.

I got the following errors while running it:


/home/krishna/QE/qe-6.2-examples/PHonon/examples/example02 : starting

This example shows how to calculate interatomic force constants in
real space for Fe.

  executables directory: /home/krishna/QE/qe-6.2/bin
  pseudo directory:  /home/krishna/QE/qe-6.2/pseudo
  temporary directory:   /home/krishna/QE/qe-6.2/tmpdir
  checking that needed directories and files exist... done

  running pw.x as:  /home/krishna/QE/qe-6.2/bin/pw.x
  running ph.x as:  /home/krishna/QE/qe-6.2/bin/ph.x
  running q2r.x as: /home/krishna/QE/qe-6.2/bin/q2r.x
  running matdyn.x as:  /home/krishna/QE/qe-6.2/bin/matdyn.x
  running plotband.x as: /home/krishna/QE/qe-6.2/bin/plotband.x
  running gnuplot as: /usr/bin/gnuplot

  cleaning /home/krishna/QE/qe-6.2/tmpdir... done
  running the scf calculation/run_exampleFe: line 152: check_failure:
command not found
 done
  running the phonon calculation /run_exampleFe: line 172:
check_failure: command not found
 done
  transforming C(q) => C(R)...STOP 1
./run_exampleFe: line 183: check_failure: command not found
 done
  recalculating omega(q) from C(R)...At line 795 of file matdyn.f90 (unit =
1, file = '�m ')
Fortran runtime error: File 'fe444.fc' does not exist
./run_exampleFe: line 202: check_failure: command not found
 done
  writing the phonon dispersions in freq.plot...STOP Error reading file
header
./run_exampleFe: line 216: check_failure: command not found
 done
  creating the postscript file fe.dispersion.ps..."gnuplot.tmp", line 24:
warning: Skipping unreadable file "freq.plot"
"gnuplot.tmp", line 24: No data in plot

./run_exampleFe: line 250: check_failure: command not found
 done
  calculating phonon DOS ...At line 795 of file matdyn.f90 (unit = 1, file
= '�Mk ')
Fortran runtime error: File 'fe444.fc' does not exist
./run_exampleFe: line 264: check_failure: command not found
 done
  generating plot of phonon_dos in the file fe.phdos.ps..."gnuplot1.tmp",
line 9: warning: Skipping unreadable file "fe.phdos"
"gnuplot1.tmp", line 9: No data in plot

./run_exampleFe: line 283: check_failure: command not found
 done

/home/krishna/QE/qe-6.2-examples/PHonon/examples/example02: done
[krishna@krishna example02]$
-


Can you please guide me with correction of the problem. Or else if there is
some example with phdos calculation of bcc iron ferrite please help me with
that.

I am including the modified set up so that you can possibly guide me with
identifying the error.

Another issue I noted is that fe.dyn1 to fe.dyn13 is created in xml format.

And q2r.out gave the error:

 Error in routine q2r (1):
 file fe.dyn1 missing!

Thanks,
Best regards,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.


run_exampleFe
Description: Binary data
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[Pw_forum] Guidance regarding calculation of fephdos of bcc iron ferrite

[Krishnendu Mukherjee]

Respected Experts,

I wish to calculate the Vibrational free energy of bcc iron ferrite using
the fqha.x command. For that I want to calculate fephdos.

 I started modifying the qe-6.2-examples/PHonon/examples/example02. The
examples was for AlAs. I modified it as far as I could.

I got the following errors while running it:

This example shows how to calculate interatomic force constants in
real space for Fe.

  executables directory: /home/krishna/QE/qe-6.2/bin
  pseudo directory:  /home/krishna/QE/qe-6.2/pseudo
  temporary directory:   /home/krishna/QE
  checking that needed directories and files exist... done

  running pw.x as:  /home/krishna/QE/qe-6.2/bin/pw.x
  running ph.x as:  /home/krishna/QE/qe-6.2/bin/ph.x
  running q2r.x as: /home/krishna/QE/qe-6.2/bin/q2r.x
  running matdyn.x as:  /home/krishna/QE/qe-6.2/bin/matdyn.x
  running plotband.x as: /home/krishna/QE/qe-6.2/bin/plotband.x
  running gnuplot as: /usr/bin/gnuplot

  cleaning /home/krishna/QE... done
  running the scf calculation/run_exampleFe: line 152: check_failure:
command not found
 done
  running the phonon calculation ...STOP 1
./run_exampleFe: line 172: check_failure: command not found
 done
  transforming C(q) => C(R)...At line 144 of file q2r.f90 (unit = 5, file =
'stdin')
Fortran runtime error: End of file
./run_exampleFe: line 183: check_failure: command not found
 done
  recalculating omega(q) from C(R)...At line 795 of file matdyn.f90 (unit =
1, file = '�� ')
Fortran runtime error: File 'fe444.fc' does not exist
./run_exampleFe: line 202: check_failure: command not found
 done
  writing the phonon dispersions in freq.plot...STOP Error reading file
header
./run_exampleFe: line 216: check_failure: command not found
 done
  creating the postscript file fe.dispersion.ps/run_exampleFe: line
250: check_failure: command not found
 done
  calculating phonon DOS ...At line 795 of file matdyn.f90 (unit = 1, file
= '�ݝ ')
Fortran runtime error: File 'fe444.fc' does not exist
./run_exampleFe: line 264: check_failure: command not found
 done
  generating plot of phonon_dos in the file fe.phdos.ps..."gnuplot1.tmp",
line 9: warning: Skipping unreadable file "fe.phdos"
"gnuplot1.tmp", line 9: No data in plot

./run_exampleFe: line 283: check_failure: command not found
 done

/home/krishna/QE/qe-6.2-examples/PHonon/examples/example02: done


Can you please guide me with correction of the problem. Or else if there is
some example with phdos calculation of bcc iron ferrite please help me with
that.

I am including the modified set up so that you can possibly guide me with
identifying the error,

Thanks,
Best regards,
Krishnendu


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.


run_exampleFe
Description: Binary data
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[Pw_forum] Problems with phonones in Fe

[Krishnendu Mukherjee]

t;*   
**
*>>*   omega( 1) = -14.768968 [THz] =-492.639743 [cm-1]
*>>*   (  0.130412   0.00-0.554126   0.00 0.419449 0.00   )
*>>*   ( -0.130412   0.00 0.554126   0.00-0.419449 0.00   )
*>> >>* Why they change their signs and how I can improve it?
*>> >>* Thank you.
*>>* Buldashev Ivan, student.
*>>* South Ural State University.
*>>* ___
*>>* Pw_forum mailing list
*>>* Pw_forum at pwscf.org <http://pwscf.org/mailman/listinfo/pw_forum>
*>>* http://pwscf.org/mailman/listinfo/pw_forum
<http://pwscf.org/mailman/listinfo/pw_forum>
*>> > > >* --
*> >* --
*>* Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
*




-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Calculation of Helmholtz free energy at a finite temperature

[Krishnendu Mukherjee]

Dear Dr. Lorenzo Paulatto,

 Thank you for your reply regarding how to find out the value for 'E(a)'
that is the ground state energy or energy of static lattice as a function
of cell parameters.

Today I have a question regarding calculation of Helmholtz free energy at a
finite temperature.

 I was going through an article titled, "Ab initio study of the
thermodynamic properties of nonmagnetic elementary fcc metals:
Exchange-correlation-related error bars and chemical trends", in Physical
Review B 76, 024309 (2007), authored by Naugebauer et al. In their method
of calculation of Helmholtz free energy there are two terms: Electronic
free energy and vibrational free energy. The electronic free energy is
composed of total energy E-total(V) at absolute temperature T=0 and a
remaining part F-el (V,T) with a 'linear dependence on V most suitable:'

F-el(V,T) = a (T) + b (T) V


Now, in Physical Review B 71, 205214 (2005) , Marzari et al. has mentioned
in Equation 7,
 Helmholtz free energy F(a, T)=E(a) + Fvib(T)
where, 'a' is geometrical degrees of freedom, 'T' is temperature, 'Fvib' is
vibrational free energy, and 'E(a)' is the ground state energy or energy of
static lattice as a function of cell parameters.

So, my question is whether the term F-el(V,T) is neglected in the Quantum
Espresso formulation of Helmholtz free energy ? In the methodology reported
by Neugebauer et al. in the above mentioned PRB (2007) article, in section
IIIA, it is mentioned that the electronic free energy was calculated using
the finite temperature formulation of DFT by Mermin. So, my other question
would be if the finite temperature formulation of DFT is included in
calculating the Helmholtz free energy in Quantum Espresso.

I should admit that as a beginner I am unable to differentiate the
methodology of quantifying vibrational free energy in the two above
mentioned publications. May be the temperature effect on electron free
energy is included in the vibrational energy formulation of QE as mentioned
in the paper of Marzari et al. (PRB 71, 205214 (2005)).

I hope I am able to explain my question.

Thanking you,
Yours sincerely,
Krishnendu


Message: 10
Date: Thu, 23 Nov 2017 08:01:09 +0100
From: Lorenzo Paulatto 
Subject: Re: [Pw_forum] Calculation of ground state energy
To: PWSCF Forum 
Message-ID:

Content-Type: text/plain; charset="utf-8"

It is just the "total energy", printed by pw.x, of course it depends on
lattice parameter

Kibd regards

--
Lorenzo Paulatto
Written on a virtual keyboard with real fingers

On 23 Nov 2017 2:17 am, "Krishnendu Mukherjee" <
krishnendu.mukherjee...@gmail.com> wrote:


Respected Experts,

 In the article PRB 71, 205214 (2005) authored by Nicolas Mounet and Nicola
Marzari, in equation 7, it is mentioned that,

Helmholtz free energy F(a, T)=E(a) + Fvib(T)

where, 'a' is geometrical degrees of freedom, 'T' is temperature, 'Fvib' is
vibrational free energy, and 'E(a)' is the ground state energy or energy of
static lattice as a function of cell parameters.

Can you please guide me how to calculate E(a)? Is there an example of it in
qe-6.2-examples?

Also I take this opportunity to thank Dr. Lorenzo Paulatto who guided me to
the appropriate examples in qe-6.2-examples to calculate the Fvib.

Thanking you,
Yours sincerely,
Krishnendu


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Calculation of ground state energy

[Krishnendu Mukherjee]

Respected Experts,

 In the article PRB 71, 205214 (2005) authored by Nicolas Mounet and Nicola
Marzari, in equation 7, it is mentioned that,

Helmholtz free energy F(a, T)=E(a) + Fvib(T)

where, 'a' is geometrical degrees of freedom, 'T' is temperature, 'Fvib' is
vibrational free energy, and 'E(a)' is the ground state energy or energy of
static lattice as a function of cell parameters.

Can you please guide me how to calculate E(a)? Is there an example of it in
qe-6.2-examples?

Also I take this opportunity to thank Dr. Lorenzo Paulatto who guided me to
the appropriate examples in qe-6.2-examples to calculate the Fvib.

Thanking you,
Yours sincerely,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Thank you for replying to my request for information regarding Computer Specification for running QE

[Krishnendu Mukherjee]

Dear Experts,

 Thank you for replying to my request for information regarding Computer
Specification for running QE.

 In response I have installed Centos 7 in my PC. It has 8 cores. During
configuration of qe-6.2 I gave the option --enable-openmp. I have run the
example01 of PW example files (qe-6.2 examples) and noticed in System
Monitor that all the cores were working.

 Increasing the RAM as advised by you and finally obtaining a LINUX
workstation as per specified by you has been noted.

Thanks a lot,
Yours sincerely,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Calculation of vibrational free energy through Quantum Espresso

[Krishnendu Mukherjee]

Dear Experts,

 I have installed qe-6.2 (openmp). I am interested in calculation of free
energy of bcc-iron (ferrite).

In the ph_user_guide.pdf it is mentioned that "Calculations of the
vibrational free
energy in the Quasi-Harmonic approximations can be performed using the QHA
package."

Is it possible to get an input file to calculate the vibrational free
energy ?

In the qe-6.2-examples.tar.gz I was unable to find example for the QHA
package. Did I miss that package somehow or it is in some earlier version
of example files?

When I give the command ./fqha.x it asks file containing the dos. If you
can guide me in making the dos file too , I can try to calculate the
vibrational free energy with the dos file. Is the dos file being asked by
the fqha.x command is density of state of phonons in specific q's?

Thanking you,
Yours sincerely,
Krishnendu


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Input file for bcc-iron (ferrite) using PWgui-6.2

[Krishnendu Mukherjee]

Respected Experts,

 Is there any available pw.x input file for bcc-iron (ferrite) in
PWgui-6.2. If not which will be most appropriate example to modify to
create a bcc-iron (ferrite) pw.x input file , e.g. (si.scf.in, or any other
example)?

Thanking you,
Yours sincerely,
Krishnendu Mukherjee


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] Computer Specification for running QE

[Krishnendu Mukherjee]

Dear Experts,

 Can you please let me know whether we always need a supercomputer to run
Quantum Espresso (QE) or a Personal Computer can do the job. If Personal
Computer is sufficient to run QE can you kindly let me know the required
configuration: Required RAM, processor speed, operating system (LINUX or
Windows), serial or parallel computation. If any other important capability
is required.

 The number of atoms required for my calculation is 50-100. And I want to
calculate both electronic and vibrational free energy.

Thanking you,
Yours sincerely,
Krishnendu Mukherjee


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] estimated scf accuracy

[Krishnendu Mukherjee]

 Respected members,

 What does "estimated scf accuracy" mean? Is there any documentation where
we can get the definition/explanation of different terms that is used in
pw.x and output files?

Thanking you,
Best regards,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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[Pw_forum] S matrix not positive definite

[Krishnendu Mukherjee]

Respected members,

 My first QE simulation failed with the following output file (please see
attached).

 Please guide me ,

Thanking you,
Sincerely,
Krishnendu


-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.


test.out
Description: Binary data
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[Pw_forum] Introduction of screw dislocation into bcc ferrite

[Krishnendu Mukherjee]

Respected members,

 Can you please guide me to include screw dislocation into bcc ferrite.

Thanking you,
Sincerely,
Krishnendu

-- 
Dr. Krishnendu Mukherjee,

Principal Scientist,
CSIR-NML,
Jamshedpur.
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