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

[Jayraj Anadani]

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
>
> Department of Systems Innovation Engineering,
> Graduate School of Science and Engineering, Iwate University
> 4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
> Phone:+81-19-621-6391
> kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
> https://sites.google.com/site/nisidatelab/
>
> ___
> 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
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Re: [QE-users] CPMD simualtion of metallic alloys upto 4 ps but RDF g(r) is not getting smooth

[Kazume NISHIDATE]

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

Department of Systems Innovation Engineering,
Graduate School of Science and Engineering, Iwate University
4-3-5 Ueda, Morioka, Iwate, 020-8551 JAPAN
Phone:+81-19-621-6391
kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/

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

[Jayraj Anadani]

Hello sir,
Actually, i am evaluating the RDF in LAMMPS  for 1 atoms in a box. and
for cp.x code in QE which is AIMD procedure, i am only taking 54 atomic
supercell according to CPMD procedure. And also , for taking 'one MD step'
of 1 atoms will take too much time to complete the simulation in cg or
damp mode of electron dynamics using cp.x code.

Thanks and regards
Jayraj Anadani

On Mon, 7 Nov, 2022, 6:19 pm Kazume NISHIDATE, 
wrote:

> Dear Jayraj Anadani
>
> > in both cases my g(r) RDF does not look smooth compared to the g(r)
> > of LAMMPS MD simulation.
>
> Did you use the same super-cell for these calculations?
>
> Look at the atomic positions of the LAMMPS you evaluated the RDF and
> convert these into the QE input format. And calculate the system using
> cp.x for 'one MD time step' and evaluate the RDF. The RDF graph must
> be the same as that of the LAMMPS. If not, there must be some wrong
> points in the RDF calculation codes.
>
> Note that:
> if you are using the same supercell and there is no wrong point in the
> RDF calculation codes, you can consider the time average of the
> quantity. The 'Ergodic theory' helps you to get the reliable smooth data.
>
>
>
> 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
> Phone:+81-19-621-6391
> kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
> https://sites.google.com/site/nisidatelab/
>
> ___
> 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
___
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Re: [QE-users] CPMD simualtion of metallic alloys upto 4 ps but RDF g(r) is not getting smooth

[Kazume NISHIDATE]

Dear Jayraj Anadani

> in both cases my g(r) RDF does not look smooth compared to the g(r)
> of LAMMPS MD simulation.

Did you use the same super-cell for these calculations?

Look at the atomic positions of the LAMMPS you evaluated the RDF and
convert these into the QE input format. And calculate the system using
cp.x for 'one MD time step' and evaluate the RDF. The RDF graph must
be the same as that of the LAMMPS. If not, there must be some wrong
points in the RDF calculation codes.

Note that:
if you are using the same supercell and there is no wrong point in the
RDF calculation codes, you can consider the time average of the
quantity. The 'Ergodic theory' helps you to get the reliable smooth data.



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
Phone:+81-19-621-6391
kazume.nishid...@gmail.com, nisid...@iwate-u.ac.jp
https://sites.google.com/site/nisidatelab/

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Re: [QE-users] Regarding antiferromagnetic state energy calculation

[Giuseppe Mattioli]

Dear Dhilshada V N (please sign always your posts with your scientific  
affiliation, too)


Ferromagnetic and antiferromagnetic coupling is related to (at least)  
two spin centers, e.g., two different metal ions. I suppose you want  
to simulate high-spin and low-spin states of a single Fe atom instead.  
If this is the case you should constrain the total magnetization of  
the system using the variable tot_magnetization (look into the pw.x  
manual for further information) to a suitable value for Fe in the  
ferrocene complex.

HTH
Giuseppe

Quoting "DHILSHADA V.N." :


Sir

I am Dhilshada V N , I am doing research in NIT Calicut.
I am studying the ferrocene system.I am using Quantum Espresso for
calculations. I want to calculate the ferromagnetic and antiferromagnetic
state energy of the system. It is possible to find the antiferromagnetic
and ferromagnetic coupling properties between two Fe atoms by considering a
supercell. But I need to calculate the FM and AFM state energies within one
Fe atom. Could you please help me sir?

Thanking you

Dhilshada V N




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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

[Jayraj Anadani]

Hello QE Community,
I am trying to simulate the metals at high temperatures (~2500K) using the
cpmd (cp.x) method. I followed this two ways, For *electron cg dynamics*
electron kinetic energy completely attaches to BO surfaces (i.e. ekinc=0)
which i run upto 1.2 ps and for *electron damp dynamics*, i maintain the
electron kinetic energy 10 times lower than the kinetic energy of ions upto
5 ps. Still, not getting smooth g(r). From the literature I found that 4ps
is enough to equilibrate the structure at a certain temperature in AIMD
simulation and randomize the structure. electron_dynamics = cg or damp in
both cases my g(r) RDF does not look smooth compared to the g(r) of LAMMPS
MD simulation.
-Is there any difference between RDF g(r) of cp.x CPMD and LAMMPS MD ?
 You can see the g(r) differences from attached files.

Regards
Jayraj Anadani
SPU Phd Scholar
[image: gr_cg.png][image: gr_damp.png]
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Re: [QE-users] oscillations in G(V) diagram

[Lorenzo Paulatto]

Hello,

first thing, I would plot the phonon dispersion sat each volume to 
verify that they are actually nice and positive. If you have internal 
degrees of freedom, and you did not relax them, it is likely that you 
got negative phonons, which definitely breaks QHA (more or less 
catastrophically, depending on how you do it).


cheers

On 06/11/2022 16:40, Jakob Kraus wrote:

Dear QE users,


thank you very much for your comments.

To clarify: I am indeed trying to work with the QHA, and the diagrams 
with the oscillations I talked about show F(V,T) + pV as a function of 
V for a given temperature.


The system in the input files is a cubic insulator, and I calculate 
the phonon contributions in F(V,T) with the help of the phonon DOS as 
generated by successive application of


ph.x, q2r.x, and matdyn.x. The combination of total energy and 
phononic contributions is done with the help of the ASE CrystalThermo 
functionality.


The calculations for the series of volumes currently use the same 
rescaled cubic unit cell, with matching rescaled atomic positions.


I will try the cell_dofree='shape' option and keep you updated. If you 
have further suggestions, feel free to add!



Best regards,


Jakob


Am 06.11.2022 um 12:00 schrieb users-requ...@lists.quantum-espresso.org:

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Today's Topics:

    1. oscillations in G(V) diagrams (Jakob Kraus)
    2. Re: oscillations in G(V) diagrams (Lorenzo Bastonero)
    3. Re: oscillations in G(V) diagrams (Lorenzo Paulatto)


--

Message: 1
Date: Fri, 4 Nov 2022 09:20:27 +0100
From: Jakob Kraus 
To: users@lists.quantum-espresso.org
Subject: [QE-users] oscillations in G(V) diagrams
Message-ID:
<68c7ecda-68e4-bf8b-68af-ea7d03063...@physik.tu-freiberg.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear QE users,


I am trying to calculate heat capacities, and to this end, I have
calculated the Gibbs energy as a function of volume

at several temperatures in a range of 0-700 K.

However, the functions that result from this do not show a single
minimum, but rather a whole lot of oscillations, which

seem to originate from the phonons, since the E(V) diagram at 0 K shows
a single minimum as expected.

I am thankful for any help you can offer with getting rid of these
oscillations.

I have attached input files and some plots to showcase the problem.


Best regards,


Jakob Kraus, TU Freiberg
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-- next part --

fildyn  =   'matdyn'
zasr    =   'crystal'
flfrc   =   'force.fc'
/
-- next part --

    calculation  = 'scf'
    title    = 'Zr_BH4_4_v95'
    verbosity    = 'high'
    restart_mode = 'from_scratch'
    tstress  = .true.
    tprnfor  = .true.
    outdir   = './'
    prefix   = 'espresso'
    pseudo_dir   = '/home/kraus/pslibrary_pp/PBE_PAW'
/

    ibrav    = 1
    ecutwfc  = 120
    ecutrho  = 960
    occupations  = 'fixed'
    nspin    = 1
    ntyp = 3
    nat  = 21
    celldm(1)    = 11.718963054402725
/

    electron_maxstep = 300
    conv_thr = 1e-10
    mixing_beta  = 0.7
/

ATOMIC_SPECIES
Zr 91.224 Zr.pbe-spn-kjpaw_psl.1.0.0.UPF
B 10.81 B.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF

K_POINTS automatic
2 2 2  0 0 0

ATOMIC_POSITIONS angstrom
Zr 3.1007040770 3.1007040770 3.1007040770
B 4.4131080846 1.7883000693 1.7883000693
B 1.7883000693 4.4131080846 1.7883000693
B 1.7883000693 1.7883000693 4.4131080846
B 4.4131080846 4.4131080846 4.4131080846
H 3.2091046915 1.6105056976 1.6105056976
H 2.9923034624 4.5909024564 1.6105056976
H 2.9923034624 1.6105056976 4.5909024564
H 3.2091046915 4.5909024564 4.5909024564
H 1.6105056976 3.2091046915 1.6105056976
H 1.6105056976 2.9923034624 4.5909024564
H 4.5909024564 2.9923034624 1.6105056976
H 4.5909024564 3.2091046915 4.5909024564
H 1.6105056976 1.6105056976 

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 have input the atomic positions in terms of supercell