Re: [QE-users] Constrained DFT with QE

[Nicola Marzari via users]

Dear Giacomo,


not that I know, beyond OS-CDFT. In here 
http://theossrv1.epfl.ch/Main/OxidationStates there is a handwaving 
description on how to implement these things by hand, but you need a 
projection on the manifold of interest, and for that currently the only 
projections afaik are on the Hubbard orbitals (there is ongoing work by 
Iurii Timrov on projections on Wannier functions).


It's not too difficult, overall, but requires a few weeks/months of 
someone strong in el-structure simulations


nicola


On 29/05/2024 13:12, Buccella Giacomo (RSE) wrote:

Dear Users,
I'd like to apply  constrained DFT (CDFT) to compute electronic coupling 
parameter within the framework of Marcus theory to get electron transfer 
rate in polyethylene.
In the work of Goldey et al 
(https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00088 
), authors 
clearly affirm that CDFT has been implemented in QE.
However, I really cannot find any reference to CDFT on QE website or 
elsewhere. As long as I know, the only CDFT module available is OS-CDFT, 
which is different and not really suitable to treat polymers.


Can anyone help me out with this?
Thank you so much in advance
Best

Giacomo

*Giacomo Buccella*
/Dipartimento Tecnologie di Trasmissione e Distribuzione/

*Ricerca sul Sistema Energetico - RSE S.p.A.*
Via R. Rubattino 54 - 20134 Milano
www.rse-web.it 
 
 


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--
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Re: [QE-users] Optimal pw command line for large systems and only Gamma point

[Nicola Marzari via users]

On 13/05/2024 17:26, Giuseppe Mattioli wrote:


    occupations= 'smearing'
    smearing= 'cold'
    degauss= 0.05 ! I know it's quite large, but necessary to 
stabilize the SCF at this preliminary stage (no geometry step done yet)

    mixing_beta= 0.4


If you want to stabilize the scf it is better to use a Gaussian smearing 
and to reduce degauss (to 0.01) and mixing beta (to 0.1 or even 
0.05~0.01). In the case of a relax calculation with a difficult first 
step, try to use scf_must_converge=.false. and a reasonable 
electron_maxstep (30~50). It often helps when the scf is not completely 
going astray.



Ciao Giuseppe, I would agree that in a semiconductor it might be more 
natural to use Gaussian (although even for cold things are now sorted 
out - 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.107.195122); but 
I wonder why reducing the smearing would help convergence.


To me, the smaller the smearing the more you can be affected by 
level-crossing instabiities?


nicola




--
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Re: [QE-users] Inquiry on Hubbard U Values for monolayer vs bulk

[Nicola Marzari via users]

Hi - you can find here an in-depth discussion:

https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.8.014007

nicola


On 30/04/2024 09:45, Zimmi Singh wrote:

Dear Developers and Users,

I am currently working on transition metal dichalcogenides and need to 
determine the appropriate Hubbard U values for my work. My question is 
whether the U value varies based on the type of magnetic order 
(paramagnetic, ferromagnetic, or antiferromagnetic) and the structure's 
thickness (monolayer vs. bulk or varying layer counts in two-dimensional 
systems), assuming identical pseudopotential, functional, and chemistry.


I have self-consistently calculated the U value for the magnetic 
monolayer. I need clarity whether the U value should be 
self-consistently calculated for the bulk magnetic and nonmagnetic 
counterparts.


Thank you for your insights.

--
*Best Regards*
Zimmi Singh
/Research_Scholar
/
/Department of Metallurgical and Materials Engineering
Indian Institute of Technology, Kharagpur
Kharagpur, India/


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Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] Effect of magnetic order on dynamic stability

[Nicola Marzari via users]

I don't think you can draw a general conclusion - a 2D material (or a 3D 
one) for a given geometry will have one or a few or many or infinite 
energy minima/selfconsistent states, where the global minimum and the 
local minima can be non-magnetic, ferromagnetic, or antiferro or 
ferrimaginetic, in primitive cells or larger supecells, or display spin 
spirals.


For a given geometry, each of this magnetic orders will lead to some 
small relaxations that can break symmetry or not, can be commensurate or 
incommensurate; ultimately, for every magnetic pattern there will be a 
supercell (maybe large, if incommensurate) in which the phonons are 
positive.


Of course, DFT or DFT+U+V or hybrids are approximate, so the 
computational truth of an approximate theory is different from reality, 
that in itself is not always truthful.


Hope this helps!

But to get a sense of the mess in which we are in, you could check this: 
https://scholar.google.ch/citations?view_op=view_citation=en=YjHKNAUJ=20=80=pubdate_for_view=YjHKNAUJ:v_xunPV0uK0C

(in press in npj computational materials).

nicola


On 09/04/2024 13:17, Zimmi Singh wrote:

Dear community and Developers,

I am reaching out to you to get some clarity regarding the dynamic 
stability of a 2D ferromagnet, 2H-VSe2. For my research, I have to 
calculate the thermal conductivity (using phono3py) of both its 
ferromagnetic and non-magnetic structures. My calculations  (using 
PBE-PAW) suggest that the ferromagnetic phase (which is the favorable 
ground state) is dynamically stable, whereas the non-magnetic phase is 
unstable with negative frequencies in the phonon dispersions for one of 
the acoustic modes.


On this topic, there are three published literature available, two 
suggesting dynamic stability for both structures 
(doi:10.1039/d2nh00429a, 10.1039/d3cp8g), whereas the third 
indicates that the non-magnetic state has one mode with negative 
frequency (doi: 10.1007/s10853-021-06311-4, Figure S6).


Should the non-magnetic counterpart of a magnet be dynamically unstable 
at zero kelvin? Can anyone shed some light on this?

--
*Best Regards*
Zimmi Singh
/Research_Scholar
/
/Department of Metallurgical and Materials Engineering
Indian Institute of Technology, Kharagpur
Kharagpur, India/


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--
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Re: [QE-users] sfc calculation for ROY structures

[Nicola Marzari via users]

Hi Nikos,


energies are relative, so nothing wrong in principle. But you cannot do 
anything meaningful if you do not study first materials simulations and 
electronic-structure methods, and try out some simple cases.


A few pointers:

https://www.materialscloud.org/learn/sections/VNL7RL/a-gentle-introduction-to-dft-calculations-april-2020

https://www.materialscloud.org/learn/sections/lfYatW/hpc-and-high-throughput-materials-modeling-ictp-trieste-2017

https://ocw.mit.edu/courses/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/

nicola


On 23/03/2024 18:03, Nikos Galanakis wrote:

Hi All,

I am very new to DFT calculations and Quantum Espresso. I am using the 
Quantum Mobile Aiida Quantum Espresso distribution to perform scf  
DFT-D3 calculations for ROY structures, however the energy I am getting 
is very low (~-4 eV). The parameters file for the calculation is the 
following:


parameters = {
   'CONTROL': {
     'calculation': 'scf',
   },
   'SYSTEM': {
     'ecutwfc': 47.,  # wave function cutoff in Ry based on the values 
of the SSSP pseudpotentials
     'ecutrho': 360.,  # density cutoff in Ry based on the values of the 
SSSP pseudpotentials

     'vdw_corr': 'DFT-D3',
   },
}

I have also selected a 4x4x4 kpoints mesh.
Can you provide any insights of what is going wrong?

Many thanks!

Nikos


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--
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Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] fail in running Koopmans

[Nicola Marzari via users]

Dear Zongyi Wang - this below from Edward Linscott:

To resolve this issue, decrease the total number of nodes allocated to 
this job; 128 is excessive. (We plan to make the workflow deal more 
intelligently with cases such as these -- see e.g. 
https://github.com/epfl-theos/koopmans/issues/196)


You mighy want to ask any further questions about the koopmans code to 
the dedicated mailing list https://groups.google.com/g/koopmans-users - 
but of course it's welcome also here.


nicola



On 23/03/2024 08:29, wangzongyi via users wrote:

Dear all
Thank you for your help last time. I am trying to use Koopmans package 
in QE7.2, however, I meet an error which I don't know how to deal with.

The program shows error:

      Error in routine  fft_type_set (6):
   there are processes with no planes. Use pencil decomposition (-pd .true.)

However, I don't konw where should I put this -pd .true. command.

My input file reads:

{
     "workflow": {
         "functional": "ki",
         "base_functional": "lda",
         "method": "dscf",
         "mp_correction": false,
         "init_orbitals": "mlwfs",
         "alpha_guess": 0.077,
         "orbital_groups": [0, 0, 0, 0, 1, 1, 1, 1],
         "pseudo_library": "pseudo_dojo_standard",
         "from_scratch": true
     },
     "atoms": {
         "cell_parameters": {
             "periodic": true,
             "ibrav": 2,
             "celldms": {"1": 10.2622}
         },
         "atomic_positions": {
             "units": "crystal",
             "positions": [["Si", 0.00, 0.00, 0.00],
                           ["Si", 0.25, 0.25, 0.25]]
         }
     },
     "kpoints": {
         "grid": [2, 2, 2],
         "offset": [0, 0, 0],
         "path": "LGXKG"
     },
     "calculator_parameters": {
         "ecutwfc": 20.0,
         "pw": {
             "system": {
                 "nbnd": 20
             }
         },
         "w90": {
             "bands_plot": true,
             "projections": [[{"fsite": [ 0.25, 0.25, 0.25 ], "ang_mtm": 
"sp3"}],
                             [{"fsite": [ 0.25, 0.25, 0.25 ], "ang_mtm": 
"sp3"}]],

                 "dis_froz_max": 10.6,
                 "dis_win_max": 16.9
},
         "ui": {
     "smooth_int_factor": 4
}
     },
     "plotting": {
         "Emin": -15,
         "Emax": 10,
         "degauss": 0.2
     }
}

and the file I sbatch my command is:

#!/bin/bash
#SBATCH -p amd_512
#SBATCH -N 1
#SBATCH -n 128
source /public3/soft/modules/module.sh
module purge
module load anaconda/2023.07-2-hxl
source activate koopmans-env
source ~/venvs/koopmans/bin/activate
module load hdf5/1.10.4-parallel-icc18 libxc/4.3.4-icc18-lcc
export PATH=/public3/home/scg9084/wzy/qe-7.2/install-ls/bin:$PATH
export PATH=/public3/home/scg9084/wzy/qe-7.2-new/qe-install/bin:$PATH
#export 
LD_LIBRARY_PATH=/public3/home/scg9084/wzy/wzy/qe-7.2/libxc-6.2.2/install/lib:$LD_LIBRARY_PATH

export PARA_PREFIX="srun"
export PARA_POSTFIX="-n 128"
koopmans si.json

Where should I add -pd .true.? Or am I supposed to change other places?
Could you please help me? Thank you very much!

Zongyi Wang


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--
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Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] Too few bands

[Nicola Marzari via users]

On 22/03/2024 13:05, aleksandr.doma--- via users wrote:

1) Is it acceptable to use SSSP library of pseudopotentials:

Materials Cloud 



Materials Cloud

Materials Cloud is built to enable the seamless sharing and 
dissemination of resources in computational mate...




with a minimum cutoff energy (which is indicated in the header of the 
pseudopotential file)?


Dear Aleksandr,


I can answer this - indeed the latest version of the PBE SSSP library 
(1.3) has been carefully verified (see this Nature Review Physics that 
came out a couple of months ago: 
https://www.nature.com/articles/s42254-023-00655-3). You can use the 
efficiency one as a default, then double check on some test case with 
the precision library if you want to be safe.


Although not tested, there is a PBEsol version also, that would be good 
to use if you deal with solids.


nicola

--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] Phonon calculation does not converge

[Nicola Marzari via users]

Out of curiosity, wouldn’t a low cutoff (not that one should use it) miss a 
ghost state (that is very localized)?

In passing, sssp pseudos are tested re not having ghosts, and have default 
suggested cutoffs. Just make sure you use the latest version 1.3

Nicola

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

On 23 Jan 2024, at 09:02, Lorenzo Paulatto  wrote:



The calculation is not only not converging, it is actually diverging. Changing 
alpha_mix and increasing nmix_ph can help, but it may also indicate something 
wrong with the calculation. I.e. a metal treated as semiconductor, or a ghost 
in the pseudopotential (which may be likely if you use norm-conservig cutoff 
with an ultrasoft dataset)

hth


On 1/23/24 08:47, Chirantan Pramanik wrote:
Hello All,

I was running Phonon for a few systems of carbonate minerals for a long time. 
Recently I used SSSP pseudopotential for PBE and faced a problem like the one 
pasted below. Optimization and SCF calculations are properly done. But phonon 
calculation is not converging. Please help. I think changing alpha_mix can be 
useful, but for my stable and optimized system, it should converge easily.

section from ph.x output:

  iter #  97 total cpu time :  1799.1 secs   av.it.:  84.0
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  1.595E+08

  iter #  98 total cpu time :  1822.7 secs   av.it.:  92.0
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  3.870E+10

  iter #  99 total cpu time :  1846.5 secs   av.it.:  92.0
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  4.585E+10

  iter # 100 total cpu time :  1869.3 secs   av.it.:  88.0
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  5.897E+09

 End of self-consistent calculation

 No convergence has been achieved


Please help in this regard.

Thanks and Regards,
Chirantan

Chirantan Pramanik
Postdoctoral Researcher
Dept. of Earth and Planetary Sciences
Weizmann Institute of Science
Rehovot, Israel



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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
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Re: [QE-users] [SPAM] Convergence issue in spin-polarized SCAN calculation

[Nicola Marzari via users]

Hi Michal,


these are two different problems - lack of convergence is not driven by 
pseudopotentials, but by algorithms. CASTEP uses a variational 
minimization, that is bound to converge, but tends to be slower - QE is 
iterative. Changing pseudopotentials might randomly make your 
calculations converge.


Generation of pseudopotential on the fly - well, you'll never know if 
they have ghost states, or how accurate they are - it's a highly 
non-linear problem.


nciola



On 25/12/2023 14:59, Husak Michal via users wrote:

Hi


I apology to QE users, but my solution:

Use instead of QE CASTEP, witch generates pseudopotentials on the fly

optimized for given functional (no databases used) ... It solves all the 
pseudopotential database issues ..

Supports rSCAN, r2SCAN ...


I hope QE authors will sometime add to the PW the on-the fly pseudopotential 
generation

functionality with no need to have external files  ...


Michal Husak

UCT Prague



From: users  on behalf of Jing Lian Ng 

Sent: Monday, December 25, 2023 2:51 PM
To: users@lists.quantum-espresso.org
Subject: [SPAM] [QE-users] Convergence issue in spin-polarized SCAN calculation

Hello all,

I am performing spin polarized calculation with SCAN functional on nickel 
oxyhydroxide system (NiOOH) and ran into convergence issue in my SCF 
calculation. Dr Yi-Min Ding reported a similar issue 
(https://lists.quantum-espresso.org/pipermail/users/2023-March/050277.html) and 
someone suggested that the issue could be due to the pseudos have been 
generated with PBE and then used with the SCAN functional. I tested NCPP from 
PseudoDojo library and SG15 library, both resulted in convergence issues when 
spin-polarized calculation is enabled. I have include the link for NCPP files 
from both libraries below, any advice would be appreciated.

NCPP for Ni, O and H:
PseudoDojo: http://www.pseudo-dojo.org/
SG15: http://quantum-simulation.org/potentials/sg15_oncv/

Thank you,
Jing Lian Ng
2nd Year PhD Student at University of Texas
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--
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Head, Laboratory for Materials Simulations, Paul Scherrer Institut
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Re: [QE-users] NMR of Metallic Systems

[Nicola Marzari via users]

On 23/11/2023 12:03, Davide Ceresoli wrote:

Dear Megan,
the orbital shift is implemented, the Knight shift no. I can't
get it to converge with respect to k-points.

Best,
Davide



Spot on! We worked on this a long time ago -
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.76.165122
and I always wondered if wannier interpolations could help - we hadn't 
the time then to try that out.


nicola



, and  
On 11/22/23 19:51, Megan Burrill wrote:

Hi,

This is a question which has been asked in years previously, but I did 
not find any recent answers. I am interested in NMR simulations using 
GIPAW of a metallic system, and was wondering if that has been 
implemented in Quantum Espresso. I appreciate any updates as to the 
status of metallic systems and the knight shift.


Thank you,
Megan Burrill

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Re: [QE-users] Stiffness Matrix

[Nicola Marzari via users]

Sure - exercise 3 of this tutorial:


Materials 
Cloud
materialscloud.org
[favicon.ico] 



Please sign with your affiliation…

Nicola

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On 20 Nov 2023, at 21:16, Elham Rezaee  wrote:



Hello everyone,

I hope this message finds you well. I am currently engaged in a project where I 
aim to calculate the elastic properties of certain crystals using Quantum 
ESPRESSO (QE) and Density Functional Theory (DFT). My primary focus is on 
determining the stiffness, stress, and strain matrices for these crystals.

Given the complexity of this task, I am reaching out to seek recommendations on 
any reliable and comprehensive sources, guides, or tutorials that can assist me 
in this process. If anyone has experience in this area or knows of resources 
that could guide me through these calculations, I would greatly appreciate your 
input.


Thank you,

Elham

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Re: [QE-users] In Phonon Calculation for Raman Spectra, How to decide to use how many unit cells?

[Nicola Marzari via users]

Dear all,

I think there is a profound misunderstanding here - make sure you understand 
the difference between primitive-cell calculations and density-functional 
perturbation theory at any arbitrary q wavevector (read 2001 RMP by Baroni et 
al) and finite-difference calculations in a supercell, a-la phonopy.

nicola


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On 12 Nov 2023, at 17:29, ludwigboltzmann.s...@nycu.edu.tw wrote:


Dear Mr. Kondrin,

Thanks, this is exactly for silicon.

Best Regards,

HY Lu

在 2023年11月12日 星期日 下午02:52:03 [GMT+8]，  寫道：


Hi, Ludwig

Raman modes should be calculate in primitive unit cell so you get the
correct number of phonon modes. In silicon you get six modes -- triply
degenerate Raman mode and three acoustic modes.

Sincerely yours,
M.V.Kondrin

On Nov 12 2023, 
ludwigboltzmann.s...@nycu.edu.tw wrote:

> Dear users: I am going to calculate Raman spectra for organic perovskite.
> (only at Gamma point)My flow chart is like this： pw.x vc-relax(geometry
> optimization)→pw.x scf→ph.x→dynmat.xIn Phonon Calculation for Raman
> Spectra , How to decide to use how many unit cells?
>
> I saw what in the tutorial, for silicon in primitive cell, Si only has 2
> atoms in a primitive cell, and the tutorial used 2 atoms (1 unit cell to
> calculate)Ref:https://www.quantum-espresso.org/wp-content/uploads/2022/03/phonons_tutorial_shanghai1.pdf
>
>
> However, according to the paper I read, the author used 4 unit cells to
> calculate, is this going to make some difference? Is it ok to
> calculate Raman spectra with on one unit cell?Difference I could imagine
> is that if I had 1unit cell with 24 atoms,With 1 unit cell (24 atoms), I
> can get 72(3*24) modes at Gamma point. With 2 unit cell (48 atoms), I can
> get 144(3*48) modes at Gamma point.  With 4 unit cell (96 atoms), I can
> get 288(3*96) modes at Gamma point.  As the unit cell increased, I would
> get more modes at Gamma point.However, it takes more time to do the
> calculation.I'm wondering what's the difference to do phonon calculation
> to use different number of unit cells? And how to decide it? Best
> Regards,HY Lu

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Re: [QE-users] Born Huang and Huang invariance conditions

[Nicola Marzari via users]

Thanks - thhis is the paper:

https://www.nature.com/articles/s41524-022-00920-6

and in the matdyn 
(https://www.quantum-espresso.org/Doc/INPUT_MATDYN.html) this is the 
option 'all'.


Not sure about q2r - should be there as well, but I do not see it - but 
maybe I'm missing something?


nicola



On 25/10/2023 16:44, Elio Physics wrote:

Dear all,

There have been several papers discussing the use of the so-called 
Born-Huang and Huang invariance conditions to soothe the possible 
negative frequencies that may arise in the long wavelength limit (q->0, 
near the G point) in the phonon dispersion of 2D and 1D material.


Is there a specific flag in the ph.x input file that needs to be turned 
on to incorporate such corrections?


Regards

Elie Moujaes
Adjunct professor level 4
Federal University of Rondonia
Brazil

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Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] can i use this trick to do faster MD calculation using pw.x ?

[Nicola Marzari via users]

Hi Jayraj,

you wrote several times, but probably many did not know where to start - 
because you are addressing several complex problems without seeming to 
have much background in the field. Answers to your 3 points:


1) you will not get anything meaningul with the low cutoffs you suggest, 
just random stuff. use the minimum cutoffs suggested in my point 2) here 
below.


2) not sure - pseudopotentials are like people, they can be messed up 
deep inside. use the SSSP 1.3 efficiency: 
https://www.materialscloud.org/discover/sssp/table/efficiency


3) not sure where to start - you need to learn and understand MD - a 
good start is if you google "ercolessi md primer"


nicola




On 18/10/2023 11:18, Jayraj Anadani wrote:

Hello, QE community!
On my metallic system, which has 128 atoms, I am running AIMD 
calculations using the pw.x code. Two pseudopotentials, PAW and USPP, 
were each tested individually. I have the following queries:


 1. For a faster AIMD calculation at a specific temperature, *Can I
perform the whole simulation with a very low "ecutwfc" and
"conv_thr" (i.e. ecutwfc=5 or 10) below a minimum cutoff of
pseudopotential? *So that I can get the next ionic position very
quickly with a fast scf cycle, then at the last MD step I will
perform a single point energy (SCF) calculation with high "ecutwfc"
and "conv_thr" to maintain a good amount of accuracy.
 2. Compared to PAW pseudopotential, USPP's convergence occurs *much
more quickly. why*? (when ecutwfc is 25)
 3. The temperature fluctuation is incredibly small and nearly equal in
the MD simulation of thousands of atoms in LAMMPS at a specific
temperature (i.e., 1000K). However, the temperature fluctuation in
MD with pw.x (AIMD) is significant, so we must set "tolp" which
stands for tolerance for velocity rescaling. Although the average
temperature is kept constant, *how closely does this significant
fluctuation match the LAMMPS MD simulation?*

Thank you

regards
JAYRAJ ANADANI
Department of Physics
SPU Research scholar

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--
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Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] Spin counting in hp.x with paramagnetic metals

[Nicola Marzari via users]

Dear Theo,


unrelated, but it's not a super good idea to describe a paramagnetic 
state with a non magnetic calculation - many paramagnetic systems have 
still strong local moments, that are disordered. At high pressure the 
local moments can disappear (e.g. iron at the ~330GPa of the 
liquid-solid boundary inside the earth), but if you are in a phase where 
they exist, and you neglect them with a non-magnetic calculation, your 
energetics will be very much off, and the volumes will not be right.


Better to use at the very least a simple AFM state, or even better a 
special quasirandom structure to choose a pattern of up/down dipoles.


nicola


On 12/09/2023 11:41, Theo Weinberger wrote:

Dear Iurii,

Yes, to be more precise I mean that when I am looking at these systems, 
I am modelling them as being nonmagnetic and so I was wondering whether 
it was the spin degeneracy that was causing this difference.


I am typically looking at pressure-induced structural transitions in 
systems with complex magnetic ground states. However, in some cases the 
exact magnetic configurations are unknown and so to simplify the problem 
(and since these structural transitions occur at high temperature in the 
paramagnetic state) I have been trying to perform the calculations in 
the nonmagnetic state. It is in these instances where I see this 
approximate doubling of U: i.e. when I allow the system to relax into a 
FM ordered state (with nspin=2) before using hp.x the value of U ends up 
being around half that of when I don’t include spin effects (nspin=1).


I hope this clarifies what I have been seeing.

Best wishes,

Theo Weinberger

PhD Student

University of Cambridge

*From:*users  *On Behalf Of 
*Iurii Timrov via users

*Sent:* Tuesday, September 12, 2023 10:31 AM
*To:* users@lists.quantum-espresso.org
*Subject:* Re: [QE-users] Spin counting in hp.x with paramagnetic metals

Dear Theo,

How do you model the paramagnetic state? Please note that "paramagnetic" 
and "nonmagnetic" state is not the same thing.


For nonmagnetic calculations there is a factor of 2 due to spin 
degeneracy when computing sums over electronic states (i.e. in charge 
density, occupation matrix, and other quantities).  If you take a 
nonmagnetic material (e.g. LiCoO2) and model it as a spin-polarized 
system (nspin=2), the value of U will be the same as when modeling it as 
nonmagetic (because the magnetization will be zero). So I do not 
understand why do you have a factor of 2 difference for U in your 
simulations.


Greetings,

Iurii

--
Dr. Iurii TIMROV
Senior Research Scientist

Theory and Simulation of Materials (THEOS)

Swiss Federal Institute of Technology Lausanne (EPFL)

CH-1015 Lausanne, Switzerland
+41 21 69 34 881

http://people.epfl.ch/265334 



*From:*users > on behalf of Theo 
Weinberger mailto:ti...@cam.ac.uk>>

*Sent:* Tuesday, September 12, 2023 11:21:03 AM
*To:* users@lists.quantum-espresso.org 


*Subject:* [QE-users] Spin counting in hp.x with paramagnetic metals

Dear Quantum Espresso Users,

I have been using the hp.x code to calculate the Hubbard-U corrections 
for correlated metallic systems in both their spin-polarised and 
paramagnetic states.


In several materials I have noticed that the Hubbard-U value determined 
for a material in its paramagnetic ground state is approximately twice 
that compared to when a spin-polarised ground state is assumed (with all 
other parameters kept the same).


I was wondering whether anyone had any insight into how the accounting 
for spins in occupied Hubbard states works for the hp.x code and whether 
the paramagnetic implementation of hp.x perhaps counts all spins states 
twice resulting in this larger value.


Thank you in advance,

Theo Weinberger

PhD Student

University of Cambridge


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Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] question about last steps of vc-relax

[Nicola Marzari via users]

Thanks Paolo!


This is a chance to remind everyone that there are sets of carefully 
tested pseudopotentials (PBE and PBEsol) with suggested cutoffs on
https://materialscloud.org/sssp ; these cover the entire periodic table. 
There are two choices - efficiency or precision. They have been verified 
again all electron calculations in https://arxiv.org/abs/2305.17274 - so 
consider these result scarefully - if your pseudopotential are not 
accueate, or cutoffs or samplings, your results will be incorrect.


The QE input generator (not yet updated to the last SSSP 1.3) gives also 
some reasonable input parameters you can always use as a sanity check 
https://www.materialscloud.org/work/tools/qeinputgenerator


nicola



On 04/09/2023 11:42, Paolo Giannozzi wrote:

On 9/4/23 11:09, Konstantin Glazyrin wrote:


An example - target relaxation pressure 600 kbar:
1 - total   stress  (Ry/bohr**3)                   (kbar)     P= 
  600.65 - last run of structure relaxation
2 - total   stress  (Ry/bohr**3)                   (kbar)     P= 
  484.28 - final scf run

May I ask - what does it indicate


it indicates that your kinetic cutoff is too low for a good description 
of the pressure



which value I should trust more and how should I proceed?


the former is the pressure, computed for the plane-wave basis set of the 
INITIAL unit cell.
The latter is the pressure, computed for the plane-wave basis set of the 
FINAL unit cell.

They should converge to the same value at sufficiently high cutoff.


Is it because of this?
SCF correction compared to forces is large: reduce conv_thr to get 
better values

For me it is conv_thr =   6.40d-06


it is a bit too large, but it is hardly related to the original problem

Paolo


Thank you!
best wishes,
             Konstantin

--
Beamline Scientist
DESY, FS-PE, bldg. 47c, L115
Notkestrasse 85
22607 Hamburg, Germany

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Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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Re: [QE-users] Fwd: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e (PBE, USPP)

[Nicola Marzari via users]

Dear Gökhan,


as far as I know there is a legacy table of old pseudopotentials:
http://pseudopotentials.quantum-espresso.org/legacy_tables/original-qe-pp-library

It's not recommended in general, but for H you can find some old Von 
Barth Car pseudos with fractional charges (maybe good to test these to 
make sure they give reasonable results).


Another very precious pseudo there is the pure Coulombic one:
H.coulomb-ae.UPF

Again, to be checked, but I believe that just chaning Zval you can also 
use it as a Cooulomb pseudo for heavier atoms, e.g. the second row from 
Li onwards, that can be useful to do all-electron tests with QE (mind 
you, for second row you easily need 1000 Ry of ecutrho).


Any comments on this actually much appreciated,


nicola


On 08/03/2023 09:13, Paolo Giannozzi wrote:

 Forwarded Message 
Subject: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e 
(PBE, USPP)

Date: Tue, 7 Mar 2023 19:58:51 +0300
From: gökhan haseki 
To: users-ow...@lists.quantum-espresso.org


Dear Quantum Espresso users, I would like to passivate the surface of a 
III-V nanowire with pseudo-Hydrogen atoms. So I need Hydrogen atom 
pseudopotential files with q=1.5e and q=0.75e (PBE, USPP). I've searched 
many pessupotential libraries but haven't been able to find it. your 
help and suggestions will guide me in this regard. Kind regards..

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Re: [QE-users] Download old versions of QE

[Nicola Marzari via users]

On 16/01/2023 15:26, Schubert Yannick via users wrote:

Dear all,


I am looking for QE version 4.1 but can not find it on the new QE 
homepage anymore. Is this code still accessible somewhere?



Best,



I have 4.0.5 and 4.3.2, but not 4.1 - happy to contribute those (would 
be great to have a historical record of the evolution of the code).


nicola



Yannick Schubert


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[QE-users] Two tenure-track positions on electronic-structure simulations (Paul Scherrer Institute, Laboratory for Materials Simulations)

[Nicola Marzari via users]

Dear QE Community,


this is to announce the opening of two tenure-track scientist positions 
in the Laboratory of Materials Simulations (https://www.psi.ch/en/lms) 
that I direct at the Paul Scherrer Institute.  These will lead to 
permanent appointments after a successful evaluation within a maximum of 
5 years.


The positions will be in the group “Materials Software and Data”, led by 
Dr. Giovanni Pizzi, and will be dedicated to the development, 
application, and dissemination of electronic-structure simulations.


All information can be found at these links below; one of the two 
position is focused on ground-state properties, and the other at 
excited-state properties:


https://www.psi.ch/en/pa/job-opportunities/55169-scientist-tenure-track-electronic-structure-simulations-of-complex

https://www.psi.ch/en/pa/job-opportunities/55172-scientist-tenure-track-electronic-structure-simulations-of-excited-state

In both cases, a key metric will be “Proven capabilities in the 
development and dissemination of advanced electronic-structure methods, 
and in their application to characterize the ground and/or excited 
states of complex materials”, together with extensive postdoctoral 
experience. The pdf of the two job ads are also linked to the Psi-k post.


Deadline for application is Jan 31 2023 - the two jobs ads are available

https://psi-k.net/wp-content/uploads/2023/01/Tenure-track-scientists-in-electronic-structure-simulations.pdf

and you'd be welcome to distribute these broadly and also directly to 
anyone interested.


Many thanks for your attention,

nicola marzari


--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
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Re: [QE-users] phonon bands shift

[Nicola Marzari via users]

It could well be correct - lo-to splitting in low symmetry systems leads to 
different limits at gamma depending on direction.

Nicola

Sent from a tiny keyboard... Contact info:
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> On 17 Sep 2022, at 15:18, Aleksandra Oranskaia 
>  wrote:
> 
> 
> Dear users and developers,
> 
> I will very appreciate any comments and suggestions on how to deal with the 
> strange step-like shifts at Gamma points. I am facing it with different 
> systems, so it is not system-specific finding.
> 
> Please see below phonons without acoustic sum rules application and with 
> "simple" rules.
> 
> Hope to hear anything.
> Thank you!
> 
> 
> -- 
> Best wishes,
> Al., phd candidate in chemical sciences
> 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
> https://cpms.kaust.edu.sa/
> 
> This message and its contents, including attachments are intended solely for 
> the original recipient. If you are not the intended recipient or have 
> received this message in error, please notify me immediately and delete this 
> message from your computer system. Any unauthorized use or distribution is 
> prohibited. Please consider the environment before printing this 
> email.___
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Re: [QE-users] gamma points calculation

[Nicola Marzari via users]

For intermediate sizes I tend to use the Baldereschi point ¼ ¼ ¼ and nosym 
.true. - unhortodox, breaks symmetry, wfc are complex, but almost as accurate 
as 2 2 2 1 1 1 at ¼ of the cost.

nicola

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> On 15 Sep 2022, at 23:48, naval singh via users 
>  wrote:
> 
> 
> Dear all,
> i have been using quantum espresso for some time and using k points i came 
> across a paper where a researcher used gamma points calculation owing to the 
> size of the cell, i wanted to know when should one use the gamma k points 
> caclculations
>  
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Re: [QE-users] Molecular dynamics calculation crashing

[Nicola Marzari via users]

Try the parameters from this, and report?

https://www.materialscloud.org/work/tools/qeinputgenerator

130Ry seems excessive, and difficult to say without knowing the other 
parameters of the run 

Sent from a tiny keyboard... Contact info:
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> On 7 Aug 2022, at 21:03, Elio Physics  wrote:
> 
> 
> Dear QE users,
> 
> I am trying to perform some molecular dynamics (MD) calculations on some 2D 
> system I am working on. The unit cell has two atoms per unit cell. I have 
> created a 3x3x1 supercell (18 atoms) ,  which will be the target of the MD 
> job.
> However, whatever I do, I keep on getting the famous 'too many bands not 
> converged..' error, with the code crashing instantly afterwards. I know that 
> this problem has been reported before. I have tried the suggested remedies:
> 
> My ecutwfc is already high (130Ry).
>  I have decreased the conv_thr to 10^(-10).
> Neither solution seems to resolve the issue. Note that , if I use the unit 
> cell (of two atoms) to perform the MD, the code works perfectly fine.
> However, it is important to perform the MD on a supercell of the material.
> 
> Any other suggestions? my version is QE-6.7
> 
> Regards and thanks in advance 
> 
> Elio Moujaess
> Adjunct professor
> Federal University of Rondonia
> Brazil
> 
> 
> 
>  
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Re: [QE-users] WFs confined within the unit-cell

[Nicola Marzari via users]

On 01/08/2022 18:03, Nicola Marzari via users wrote:
or between different unit cells. 


Apologies - I meant:

--> or between different MLWFs in different unit cells.

nicola


--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] WFs confined within the unit-cell

[Nicola Marzari via users]

Dear Emanuel,


a few pointers here:

- in the calculations, you have a real space unit cell A (whatever it 
is; it can be the primitive one, or a larger one); its corresponding 
Brillouin Zone B is sampled with a k1xk2xk3 monkhorst-pack mesh, with 
k1/k2/k3 integers. In principle, k1/k2/k3 are integers that should be 
very large/go to infinity; in practice they are finite, but large enough 
to make sure your calculations are converged.


- the MLWFs live in a supercell S that is k1xk2xk3 times larger than the 
unit cell A of your calculation. The MLWFs are by definition periodic 
with the periodicity of this supercell S. If S is large enough (i.e. if 
the combination of your unit cell A and your k-sampling is fine enough - 
e.g. primitive with 8x8x8 sampling, for silicon, or - exactly 
equivalently - a unit cell A double the primitive one in each direction, 
and 4x4x4 sampling), the MLWFs will be able to decay to almost zero 
before they rise again (since, remember, they are in themselves periodic 
with the periodicity of S).


- the MLWFs will have the localization that the physics of the system 
tells them to have (I'm assuming here we are dealing with MLWFs in an 
insulator, obtained transforming the valence bands). They will be 
localized, but typically do not got to zero from their maximum after a 
distanca as short as a half primitive cell. Much longer. But they do 
decay exponentially.


- an interesting quantity to monitor is the matrix element of your 
operator of choice (e.g. the Hamiltonian) between the same MLWFs, but 
localized in different unit cells, or between different unit cells. Of 
course, once the unit cells get very far away, these matrix elements 
with rise again, because of the overall periodicity in S for the MLWFs


Some of these issues were discussed in here
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.95.076804
but are explained better in Young-Su Lee PhD thesis - see e.g. Fig 4.11 
and 4.14 in https://dspace.mit.edu/handle/1721.1/37371


Hope this clarifies some of your doubts - important to make sure you 
master the points above if you want to work on this topic. The Rev Mod 
Phys from 2012 might be also a good starting point, with its 
introductory sections:

https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.84.1419


nicola


On 01/08/2022 15:19, EMANUEL ALBERTO MARTINEZ wrote:

Hello everyone,

I have a simple question regarding to the localization of WFs. It seems 
to be intuitive that an individual spread for each MLWF less than the 
size of unit-cell ensures that it is localized well-within the 
unit-cell. I need to justify some models I'm creating and I recently 
realized that It could exist rare systems in which the MLWFs can surpass 
the size of the unit-cell or even have another periodicity. These cases 
will break my approximations. Could you give me any references about the 
spread values and the localization within the unit-cell? I know It could 
sound senseless, but I need to make it as clear as possible.


Thanks in advance!

--

Emanuel A. Martínez

Departamento de Física de Materiales

Universidad Complutense de Madrid



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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Advanced Quantum ESPRESSO tutorial: Hubbard and Koopmans functionals from linear response

[Nicola Marzari via users]

Very nice! If you haven't already posted to Psi-k, highligt keynote 
speakers early on



On 29/07/2022 11:02, Iurii TIMROV via users wrote:

Dear Quantum ESPRESSO community,


We are pleased to announce the "Advanced Quantum ESPRESSO tutorial: 
Hubbard and Koopmans functionals from linear response".



**

*

Dates:9-11 November 2022

Format:Online

Registration fee: 0 (free of charge)

Deadline for applications:1 October 2022

Website of the event:https://sites.google.com/view/hubbard-koopmans 


*


**

*

The goal of this tutorial is to introduce PhD students, postdocs, and 
junior scientists to the use of advanced functionals aimed at modeling 
complex materials, such as the extended Hubbard and Koopmans 
functionals. By eliminating self-interaction errors and restoring total 
energy piecewise linearity, these advances broaden the scope of DFT by 
either improving the ground-state description of transition-metal and 
rare-earth compounds or by giving access to accurate spectral properties 
(like fundamental band gaps and band structures). Their actual 
implementation also takes advantage of linear-response theory through 
the self-consistent incarnation contained in density-functional 
perturbation theory. The first day of the tutorial will be devoted to an 
introduction to fundamental aspects of DFT using local and semi-local 
functionals, its application to materials science and physics, and its 
limitations. In the next 2 days, the tutorial will cover the theoretical 
framework of Hubbard and Koopmans functionals (the main topic of this 
event) and their applications to representative case studies. The 
reference computational platform of the tutorial will be Quantum 
ESPRESSO, a widely used open-source electronic-structure software, which 
implements both extended Hubbard and Koopmans functionals.



If attending the Psi-k conference in Lausanne, feel free to come and see 
us at the MARVEL and MaX booths to learn more about the virtual tutorial 
and the codes involved.


*
*

Keynote speakers:

Leoor Kronik (Weizmann 
Institute of Science, Israel)


Renata Wentzcovitch 
(Columbia 
University, USA)


Matteo Gatti (École 
Polytechnique, France)


*
*

Lecturers:

*

**

*

Nicola Marzari (EPFL and PSI, 
Switzerland)


Giovanni Pizzi (EPFL and PSI, 
Switzerland)


Edward Linscott (EPFL, Switzerland)

Iurii Timrov (EPFL, Switzerland)

Nicola Colonna (PSI, 
Switzerland)


Andrea Floris (Lincoln University, UK)

Andrea Ferretti (CNR Modena, Italy)

***
**

**Matteo Cococcioni 
(University of 
Pavia, Italy)**




**

*

Yours sincerely,

Iurii Timrov, Nicola Colonna, Matteo Cococcioni, and Andrea Ferretti

*


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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
___
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Re: [QE-users] vdW not implemented for nspin > 1 in QE 6.5

[Nicola Marzari via users]

Also, stress can always be verified by looking at the numerical derivative of 
an energy vs strain curve, making sure the cutoffs on wfc and rho are large 
enough so that the stress tensor is converged.

Nicola

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

> On 27 Jun 2022, at 16:01, Giuseppe Mattioli  
> wrote:
> 
> 
> It is not even a "problem". vdwdf stress and even vdwdf scf with nspin=2 have 
> been implemented only lately, after the publication of PRL 115, 136402 (2015) 
> for sure in the case of scf. The solution is to update QE to a newer version, 
> possibly the newest, as suggested by Kazume. If you don't want to use it, you 
> may try with vdw_corr='grimme-d3', that is, a totally different 
> implementation of dispersion forces, with pros & cons and assuming you are 
> aware of the differences.
> HTH
> Giuseppe
> 
> Quoting EMANUEL ALBERTO MARTINEZ :
> 
>> Ok. I will try it, again ,it was a little hard to install the latest
>> version by several incompatibilities I found.
>> 
>> 
>> Regards
>> 
>>> El lun, 27 jun 2022 a las 14:40, Kazume NISHIDATE ()
>>> escribió:
>>> 
>>> 
>>> > 2022/06/27 20:24、EMANUEL ALBERTO MARTINEZ のメール:
>>> >
>>> >  I am using QE v6.5 in a HPC cluster. Could anyone please help me to
>>> solve this problem?
>>> 
>>> 
>>> First, you should update your QE to v.7.1.
>>> (So that we can follow your question.)
>>> 
>>> 
>>> 西館
>>> Kazume NISHIDATE Ph.D
>>> 
>>> ___
>>> 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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>>> users mailing list users@lists.quantum-espresso.org
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> 
> 
> 
> 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: 
> 
> ___
> 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,
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Re: [QE-users] Is it acceptable to neglect spin, magnetism and U for CPMD simulation of iron oxides (Fe2O3, Fe3O4 and FeO)

[Nicola Marzari via users]

Thanks Giuseppe,


couldn't agree more! Never being one to miss an opportunity to promote 
dft+hubbard, I would also add that these functional can be also more 
accurate, because they screen a fock-like term with awareness of the 
local bonding - see Iurii's just-out work on batteries:

https://arxiv.org/abs/2203.15732

nicola

On 07/04/2022 12:39, Giuseppe Mattioli wrote:


Dear Kejiang

Only EXX functionals such as PBE0 or HSE significantly increase the 
computation time. DFT+U has been primarily developed as a cost-effective 
method to correct delocalization errors in the case of localized shells 
such as those present in transition metal oxides. There are tons of 
literature on this... In my opinion (and I've investigated several 
similar system with the same purpose) you cannot neglect U, spin if 
you want to obtain meaningful (i.e., publishable...) results. cp.x can 
manage open shell systems with a fixed magnetic moment within the DFT+U 
framework. But you must carefully setup and test your calculations, 
which are a bit on the "nonstandard" side.

HTH
Giuseppe

Quoting likeji...@ustb.edu.cn:


Dear QE-Users,

I am planning to do some CPMD simulation about iron oxides (Fe2O3, 
Fe3O4 and
FeO) and their reactions with hydrogen at high temperature using cp.x 
of QE

7.0.

As it is well known that spin and magnetism are the most fundamental
characteristics for iron and its oxides, we should consider them (spin 
and

magnetism) and add U in many cases for 'scf' or 'relax'/'vc-relax'
calculations with pw.x.  But it seems that considering spin, magnetism 
and U
will make things more complicated and significantly increase the 
computation
time, I am wondering whether it is acceptable to neglect spin, 
magnetism and

U for CPMD simulation of iron oxides (Fe2O3, Fe3O4 and FeO) and their
reactions with Hydrogen gas. My goal is only to try to simulation the
reduction process in atomistic scale, and the CPMD trajectory results are
sufficient to capture the reduction mechanism while the accuracy of band
gap, magnetism is not the focus of my study.

Any comments or suggestions will be much appreciated.

Thanks,
Kejiang

-
Dr. Kejiang Li
School of Metallurgical and Ecological Engineering,
University of Science and Technology Beijing
Xueyuan Rd., Haidian District, Beijing 100083, P. R. China
https://kejiangli.com/




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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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Slow convergence

[Nicola Marzari via users]

Thanks Paolo!

Max - you say you are using the pseudos from 
http://theossrv1.epfl.ch/Main/Pseudopotentials, but you are actually not.


There is a sentence at the beginning of that page, in  very large fonts, 
that that tells you what to use - and then there is a long list of other 
entries, in small fonts, labeled as "older material, kept for 
reference", not "thoroughly tested".


My personal advice on what it takes to do a semi decent calculation it's 
at this link:


http://theossrv1.epfl.ch/Main/SetupForQuantumESPRESSOCalculations

nicola


On 24/03/2022 12:22, Paolo Giannozzi wrote:
It seems to work (= to yield apparently sensible results) if 
W.pbe-spn-rrkjus_psl.0.2.3.UPF is replaced by 
W.pbe-spfn-rrkjus_psl.1.0.0.UPF (but not by W.pbe-spn-rrkjus_psl.1.0.0.UPF)


Paolo

On Thu, Mar 24, 2022 at 11:30 AM Paolo Giannozzi > wrote:


The convergence is not "slow", it's non-existent. There is nothing
wrong in your input: self-consistency starts well. Note however what
happens at iteration 6: there is an abnormally large jump in the scf
error. The only reason I can think of is that one of the
pseudopotentials is bad (bad = has a ghost state) . Try to change
pseudopotentials, one at the time.

Paolo

On Mon, Mar 21, 2022 at 9:50 PM Максим Арсентьев
mailto:ars21031...@gmail.com>> wrote:

Hello everyone. I am trying to perform a vc-relax run using the
pw.x code for tungsten niobate. I use ultrasoft pbe files from
http://theossrv1.epfl.ch/Main/Pseudopotentials
 . The
convergence is slow. Is something wrong in my input file

Best wishes,
Max


  
     prefix='NbWO',
     calculation = 'vc-relax',
     restart_mode = 'from_scratch'
     pseudo_dir='/home/mxm2/Documents/internal_and_full_opt/NbWO',
     outdir =
'/home/mxm2/Documents/internal_and_full_opt/NbWO/temp',
     forc_conv_thr = 3.8d-4 ,
     nstep = 99,
     etot_conv_thr = 1.0d-4 ,
  /
  
     ibrav=  0, nat= 122, ntyp= 3,
     celldm(1)=1.889726,
     ecutwfc = 35.0,
     occupations ='smearing', smearing ='gaussian',
     degauss=0.02,
  /
  
     conv_thr = 1e-6,
     mixing_beta=0.3,
     electron_maxstep=500
  /
  
  /
   
  /
ATOMIC_SPECIES
Nb   92.906    Nb.pbe-spn-rrkjus_psl.0.3.0.UPF
O    15.999     O.pbe-n-rrkjus_psl.0.1.UPF
W   183.84      W.pbe-spn-rrkjus_psl.0.2.3.UPF
ATOMIC_POSITIONS (crystal)
Nb 0.46384 0.37332 0.46914
Nb 0.53616 0.62668 0.46914
Nb 0.30402 0.28755 0.50016
Nb 0.69598 0.71245 0.50016
Nb 0.78727 0.194 0.99492
Nb 0.21272 0.806 0.99492
Nb 0.71678 0.94725 0.99154
Nb 0.28322 0.05275 0.99154
Nb 0.44538 0.78418 0.50708
Nb 0.55462 0.21582 0.50708
Nb 0.60646 0.87207 0.48962
Nb 0.39354 0.12793 0.48962
Nb 0.37259 0.89382 0.00976
Nb 0.62741 0.10618 0.00976
Nb 0.96384 0.87332 0.96914
Nb 0.03616 0.12668 0.96914
Nb 0.80402 0.78755 0.00016
Nb 0.19598 0.21245 0.00016
Nb 0.28728 0.694 0.49492
Nb 0.71273 0.306 0.49492
Nb 0.21678 0.44725 0.49154
Nb 0.78322 0.55275 0.49154
Nb 0.94538 0.28418 0.00708
Nb 0.05462 0.71582 0.00708
Nb 0.10646 0.37207 0.98962
Nb 0.89354 0.62793 0.98962
Nb 0.87259 0.39382 0.50976
Nb 0.12741 0.60618 0.50976
O 0.46597 0.3783 0.99454
O 0.53403 0.6217 0.99454
O 0.86959 0.03688 0.50851
O 0.13041 0.96312 0.50851
O 0.91584 0.95689 0.00346
O 0.08416 0.04311 0.00346
O 0.45097 0.58093 0.50343
O 0.54903 0.41907 0.50343
O 0.38249 0.32729 0.49949
O 0.61751 0.67271 0.49949
O 0.82643 0.11647 0.99726
O 0.17357 0.88353 0.99726
O 0.79094 0.992 0.99589
O 0.20906 0.008 0.99589
O 0.49061 0.70902 0.50312
O 0.50939 0.29098 0.50312
O 0.28502 0.27115 0.99848
O 0.71498 0.72885 0.99848
O 0.77143 0.21412 0.49854
O 0.22857 0.78588 0.49854
O 0.75631 0.86378 0.99729
O 0.24369 0.13622 0.99729
O 0.36389 0.74402 0.5024
O 0.63611 0.25598 0.5024
O 0.69451 0.93577 0.49434
O 0.30549 0.06423 0.49434
O 0.43555 0.80655 0.00484
O 0.56445 0.19345 0.00484
O 0.65356 0.79887 0.49582
O 0.34644 0.20113 0.49582
O 0.29982 0.84627 0.00333
O 0.70017 0.15373 0.00333
O 0.6236 0.89265 0.9933
O 0.3764 0.10735 0.9933
O 0.39318 0.87688 0.50597
O 0.60682 0.12312 0.50597
O 0.5611 0.96377 0.49359
O 0.4389 

Re: [QE-users] Pseudopotentials for all-electron DFT calculations

[Nicola Marzari via users]

Hopefully this one

http://pseudopotentials.quantum-espresso.org/upf_files/H.coulomb-ae.UPF

and you just change the z valence. By the time you get to carbon (zval 6) you 
are looking at 500-1000 Ry of ecutwfc

Nicola

Sent from a tiny keyboard... Contact info:
http://theossrv1.epfl.ch/Main/Contact

> On 10 Mar 2022, at 00:13, John McFarland via users 
>  wrote:
> 
> 
> I would like to do some simple all-electron DFT calculations. Does anyone 
> know where I might get pseudopotentials for this? I'm basically looking for 
> point charge nuclei.
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Re: [QE-users] banduppy for band unfolding

[Nicola Marzari via users]

Dear Kenneth,


there is a very comprehensive tool to obtain k-point paths that are 
compliant with the guidelines from the international union of 
crystallography - I strongly recommed you use those.


You can find it online here:
https://www.materialscloud.org/work/tools/seekpath

with also links to the paper and the relevant python library.

nicola


On 02/03/2022 18:04, kenneth senados wrote:

Dear QE Users,

I am studying the tutorial files for banduppy used for band unfolding.

I would like to ask how this "K_POINTS  crystal" below has been 
generated. I tried kpoints.x but the kpoints below does not match with 
the output of kpoints.x


-
K_POINTS crystal
84
   0.    0.    0.    1
   0.    0.03846154    0.    1
   0.    0.07692308    0.    1
   0.    0.11538462    0.    1
   0.    0.15384615    0.    1
   0.    0.19230769    0.    1
   0.    0.23076923    0.    1
   0.    0.26923077    0.    1
   0.    0.30769231    0.    1
   0.    0.34615385    0.    1
   0.    0.38461538    0.    1
   0.    0.42307692    0.    1
   0.    0.46153846    0.    1
   0.    0.5000    0.    1
   0.    0.53846154    0.    1
   0.    0.57692308    0.    1
   0.    0.61538462    0.    1
   0.    0.65384615    0.    1
   0.    0.69230769    0.    1
   0.    0.73076923    0.    1
   0.    0.76923077    0.    1
   0.    0.80769231    0.    1
   0.    0.84615385    0.    1
   0.    0.88461538    0.    1
   0.    0.92307692    0.    1
   0.    0.96153846    0.    1
   0.02272727    0.02272727    0.02272727    1
   0.02678571    0.02678571    0.    1
   0.03125000    0.    0.03125000    1
   0.04545455    0.04545455    0.04545455    1
   0.05357143    0.05357143    0.    1
   0.0625    0.    0.0625    1
   0.06818182    0.06818182    0.06818182    1
   0.08035714    0.08035714    0.    1
   0.09090909    0.09090909    0.09090909    1
   0.09375000    0.    0.09375000    1
   0.10714286    0.10714286    0.    1
   0.11363636    0.11363636    0.11363636    1
   0.1250    0.    0.1250    1
   0.13392857    0.13392857    0.    1
   0.13636364    0.13636364    0.13636364    1
   0.15625000    0.    0.15625000    1
   0.15909091    0.15909091    0.15909091    1
   0.16071429    0.16071429    0.    1
   0.18181818    0.18181818    0.18181818    1
   0.1875    0.    0.1875    1
   0.1875    0.1875    0.    1
   0.20454545    0.20454545    0.20454545    1
   0.21428571    0.21428571    0.    1
   0.21875000    0.    0.21875000    1
   0.22727273    0.22727273    0.22727273    1
   0.24107143    0.24107143    0.    1
   0.2500    0.    0.2500    1
   0.2500    0.2500    0.2500    1
   0.26785714    0.26785714    0.    1
   0.27272727    0.27272727    0.27272727    1
   0.29464286    0.29464286    0.    1
   0.29545455    0.29545455    0.29545455    1
   0.31818182    0.31818182    0.31818182    1
   0.32142857    0.32142857    0.    1
   0.34090909    0.34090909    0.34090909    1
   0.34821429    0.34821429    0.    1
   0.36363636    0.36363636    0.36363636    1
   0.3750    0.3750    0.    1
   0.38636364    0.38636364    0.38636364    1
   0.40178571    0.40178571    0.    1
   0.40909091    0.40909091    0.40909091    1
   0.42857143    0.42857143    0.    1
   0.43181818    0.43181818    0.43181818    1
   0.45454545    0.45454545    0.45454545    1
   0.45535714    0.45535714    0.    1
   0.47727273    0.47727273    0.47727273    1
   0.48214286    0.48214286    0.    1
   0.5000    0.5000    0.5000    1
   0.50892857    0.50892857    0.    1
   0.53571429    0.53571429    0.    1
   0.5625    0.5625    0.    1
   0.58928571    0.58928571    0.    1
   0.61607143    0.61607143    0.    1
   0.64285714    0.64285714    0.    1
   0.66964286    0.66964286    0.    1
   0.69642857    0.69642857    0.    1
   0.72321429    0.72321429    0.    1
   0.7500    0.7500    0.    1


any help is much appreciated.

Thank you.

Best regards,

Ken

Disclaimer:
/The information in this electronic message is privileged and 
confidential, intended only for use of 

Re: [QE-users] Defining C diamond structure cp.x

[Nicola Marzari via users]

Dear Juniper,

if your long-term goal is to study warm dense matter, you want to do 
molecular dynamics simulations with CP or PW in a large supercell, and 
with no symmetry (ibrav=0). Of course, if you want to learn how to do 
calculations (it's a long and winding road) you could practive diamond, 
with ibrav=2 for fcc, and 2 atoms per unit cell.


A GUI for converting from CIF to various QE inputs would be invaluable 
to me and I would greatly appreciate access to such a resource.
There has been one around for a while, using the ASE and pymatgen 
converters - neither of them, admittedly, extensively tested (I would 
trust ASE more):


https://www.materialscloud.org/work/tools/qeinputgenerator

nicola


--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
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Re: [QE-users] LDA normconserving pseudopoential Cu

[Nicola Marzari via users]

Dear Johannes,

There are a couple of standard ones to look at - both 
multiple-projectors norm conserving (ONCV) - not sure if the raman code 
in qe is compatible with them.


One set is the Schlipf-Gygi:
http://www.quantum-simulation.org/potentials/sg15_oncv/

that is tested e.g. by us:
https://www.materialscloud.org/discover/sssp/

Cu seems to work quite well at 90/360 Ry cutoffs for wavefunctions and 
charge density.


The ohter one is pseudo-dojo: http://www.pseudo-dojo.org, curated  by 
the Abinit group.


Both sets are undergoing stricter verification as part of the "common 
workflows" project - but I would already be confident on using what 
there is.


The other option is to calculate Raman using the electric-enthalpy 
approach (see I think Umari et al in the past), and then you are not 
constrained to norm-conserving pseudopotentials.


nicola



On 08/02/2022 13:17, Johannes Meusburger - STFC UKRI via users wrote:

Dear all,

I want to simulate the Raman spectrum of a Copper-oxide compound using 
Quantum EPSRESSO. As far as I know, this is merely possible using 
norm-conserving PP on the LDA level of theory. Therefore, I have 
downloaded on the pz.0.3.1 folder from the THEOS website(THEOS 
Main/Pseudopotentials (epfl.ch) 
), which unfortunately 
does not contain any norm-conserving pseudopotential for Cu. I also had 
a look on the Quantum ESPRESSO website where I also could not find such 
a pseudopotential in any of the databases. Does anyone know any sources 
where I could obtain a NC PP for LDA calculations that works with 
Quantum ESPRESSO?


Many thanks and all the best,

Johannes

Johannes Meusburger
ISIS Neutron and Muon Source, UK

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Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Enquiry about electron-phonon calculation

[Nicola Marzari via users]

On 06/12/2021 08:59, Lorenzo Paulatto wrote:
Yet it is possible. You need a very goo representation of the Fermi 
surface in order to identify the possible el-ph processes, but such a 
fine grid is not required to have good phonons.


Also note that there are at least two QE packages to do el-ph 
calculation with Wannier interpolation : epik by M Calandra and EPW by F 
Giustino




Thanks Lorenzo - maybe just for completeness I should add the other two 
I know of (to 4 altogether - an embarassment of riches...):


Perturbo: https://perturbo-code.github.io/
Phoebe: https://arxiv.org/abs/2111.14999

Also, I do not think epik is available open-source somewhere, correct?

nicola



regards

--
Lorenzo Paulatto - Paris
On Dec 6 2021, at 3:27 am, Elio Physics  wrote:

Dear all,

As is well known in electron-phonon calculations, one has to do a
self consistent (scf) calculation over a dense electronic grid
followed by an scf calculation on a coarse grid.
The electron phonon calculation is usually performed after
calculation the vibrational frequencies for each point.

My question is : If we increase the dense grid, Is it possible (Is
there a way in QE) to compute the el-ph coefficients without
recomputing the dynamical files (vibrational frequencies), which
actually depend on the coarse grid.  This would save a lot of time.

Thanks in advance

Ellie Moujaes
Federal Universil of Rondonia
Brazil
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Sent from Mailspring

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--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Oscillating volume in VC-MD

[Nicola Marzari via users]

Dear Andrii,

maybe the small oscillations are not so important, depending on what you 
want to achieve. If you are really keen on investigating further, you 
could do a fairly short run using MD with fixed cell, and average the 
stress tensor over that run - 1/3 of the trace would tell you how 
compressed or expanded your cell seems to be. Then, knowing the bulk 
modulus (ok to use the zero-T one you get from an equation of state) you 
would know how much to isotropically strain the cell so that on average 
it will not want to contract or expand.


nicola


On 22/11/2021 19:49, Andrii Shyichuk wrote:

Dear Nikola,

Thank you for the suggestion.

The system is a lutetium oxide cell of 80 atoms, a moderately symmetric 
crystal.


You are absolutely right, the initial geometry has the pressure 
components of 0.01-0.03 kbar.

Does it make sense to try and optimize it until the pressure is zero?

 From this paper I can tell that Nose-Hover approach is a kind of 
thermostat, which (apparently) is not implemented in QE for VC-MD.

https://aip.scitation.org/doi/pdf/10.1063/1.463940
I will look into it, but I was hoping for a QE-based solution.

Also, I've found the Wentzcovitch paper to be a very interesting read,
https://journals.aps.org/prb/pdf/10.1103/PhysRevB.44.2358

Here it is stated that Wentzcovitch cell dynamics uses the Lagrangian 
from that paper:

https://lists.quantum-espresso.org/pipermail/users/2007-August/007052.html

I've ran some tests with Wentzcovitch cell dynamics to see if it helps.
Apparently, not quite: the cell also oscillates, albeit at a much lower 
frequency.
Actually, the Wentzcovitch dynamics (cell_dynamics='w') n_step-volume 
curve looks like an oscillating envelope of the Parrinello-Rahman 
dynamics (cell_dynamics='pr') n_step-volume curve.


Best regards.
Andrii




Date: Thu, 18 Nov 2021 17:21:10 +0100
From: Nicola Marzari 
To: users@lists.quantum-espresso.org
Subject: Re: [QE-users] Oscillating volume in VC-MD
Message-ID: <93c39f9e-473d-1c31-c0bb-00eb19123...@epfl.ch>
Content-Type: text/plain; charset=UTF-8; format=flowed



Dear Andrii,


this might be related to the fact that the more harmonic a system is,
the more difficult it is to thermalize it - since it's anharmonicity
that shuffles excitations.

[If you have a system of harmonic oscillators, the populations are good
quantum numbers, i.e. they are constant of motions. A good starting
point is the literature about Nose-hoover chains, disucssing these
difficulties in thermalization.]

In your case, you have low-ish temperatures, and you start from a cell
that has probably a small non-zero pressure, so it oscillates for a long
time like a pendulum around its equilibrium volume, with very weak
couplings.

    nicola



On 18/11/2021 16:45, Andrii Shyichuk via users wrote:

Dear Users,

I am running a VC-MD calculation where the cell volume oscillates in a
nice sinusoidal way, with the period of about 250 fs.
The oscillations are in the range of 99.5-101.5% of the initial volume
for 300K, and within 99-102.5% for 500K.

That happens both with 5 fs (dt=103.353) and 0.5 fs (dt=10.33534) time
steps.
The tolp was 10 in the first case and 2 in the second case.

I use ion_temperature = 'rescaling',? cell_dynamics = 'pr', ion_dynamics
= 'beeman' and nraise = 1.

I've tried searching the mailing archive and found nothing relevant.

Is it normal? Shouldn't the volume converge to a certain value?


Thank you in advance.
Best regards.
Andrii Shyichuk, University of Wroc?aw
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Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact





--
--
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Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Oscillating volume in VC-MD

[Nicola Marzari via users]

Dear Andrii,


this might be related to the fact that the more harmonic a system is, 
the more difficult it is to thermalize it - since it's anharmonicity 
that shuffles excitations.


[If you have a system of harmonic oscillators, the populations are good 
quantum numbers, i.e. they are constant of motions. A good starting 
point is the literature about Nose-hoover chains, disucssing these 
difficulties in thermalization.]


In your case, you have low-ish temperatures, and you start from a cell 
that has probably a small non-zero pressure, so it oscillates for a long 
time like a pendulum around its equilibrium volume, with very weak 
couplings.


nicola



On 18/11/2021 16:45, Andrii Shyichuk via users wrote:

Dear Users,

I am running a VC-MD calculation where the cell volume oscillates in a 
nice sinusoidal way, with the period of about 250 fs.
The oscillations are in the range of 99.5-101.5% of the initial volume 
for 300K, and within 99-102.5% for 500K.


That happens both with 5 fs (dt=103.353) and 0.5 fs (dt=10.33534) time 
steps.

The tolp was 10 in the first case and 2 in the second case.

I use ion_temperature = 'rescaling',  cell_dynamics = 'pr', ion_dynamics 
= 'beeman' and nraise = 1.


I've tried searching the mailing archive and found nothing relevant.

Is it normal? Shouldn't the volume converge to a certain value?


Thank you in advance.
Best regards.
Andrii Shyichuk, University of Wrocław
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Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] How to improve the values calculated using QE?

[Nicola Marzari via users]

Dear Tarik,

QE, VASP, Wien2K, give all the same result - the DFT result.

You need to do the calculations properly, and all-electron methods like 
Wien2K are more suited to high accuracy, at the expense of complexity 
and computational costs.


But at the end you cannot do DFT simulations without a supervisor, 
and/or some training. Many places where to start, e.g.

https://www.quantum-espresso.org/resources/tutorials
with a brief overview here:
https://www.materialscloud.org/learn/sections/VNL7RL/a-gentle-introduction-to-dft-calculations-april-2020

nicola

On 11/11/2021 19:45, Tarik wrote:

Thank you for responding, Nicola.

Yes I understand, we cannot do much in QE but I was wondering if 
changing ecutrho or ecutwfc might bring better results or some other 
parameter can be changed.


I heard Wein2k or VASP gives more accurate results? Infact, most of the 
papers (literature) say that they use VASP for computing. Why is that 
so? I do not want to believe Quantum Espresso is anything less.


Also, can you please tell me how to implement different approximations 
in QE? Say for example, I want to use the GGA-PBE or the PBE-sol 
approx., how do I incorporate that in my input code?


Tarik

On Thu 11 Nov, 2021, 11:56 PM Nicola Marzari, <mailto:nicola.marz...@epfl.ch>> wrote:



Blush :-)

                         nicola


On 11/11/2021 19:25, Stefano Baroni wrote:
 > Actually, at a closer look, and under any lighting, you are much
more
 > handsome than Brad Pitt. SB
 >
 >> On 11 Nov 2021, at 19:21, Nicola Marzari via users
 >> mailto:users@lists.quantum-espresso.org>
 >> <mailto:users@lists.quantum-espresso.org
<mailto:users@lists.quantum-espresso.org>>> wrote:
 >>
 >>
 >>
 >> Dear Tarik,
 >>
 >>
 >> DFT is not a theory that describes electronic excitations -
there is
 >> only the total charge density in DFT, and it describes the
ground state.
 >>
 >> If you use Kohn-Sham DFT to approximate the kinetic energy
functional
 >> introducing the non-interacting Kohn-Sham particles, these lead to
 >> band dispersions that look a bit like the quasiparticle excitations
 >> you are looking for.
 >>
 >> Here, "look like" is in the same sense that I look like Brad Pitt,
 >> under proper lightning. A fleeting illusion, that can be
occasionally
 >> oversold as a viable approximation. But 1.18 eV is what it is,
at the end.
 >>
 >> There is not much that we can do, a part from switching to theories
 >> and methods that describe electronic excitations.
 >>
 >> Hope this helps,
 >>
 >> nicola
 >>
 >>
 >>
 >> On 11/11/2021 19:03, Tarik wrote:
 >>> Dear Experts,
 >>> Kindly go through my preceding mail and suggest ways to make the
 >>> obtained values better. It is really important to me.
 >>> Thanking you,
 >>> Tarik
 >>> On Thu 11 Nov, 2021, 9:43 AM Tarik, mailto:bitrin...@gmail.com>
 >>> <mailto:bitrin...@gmail.com
<mailto:bitrin...@gmail.com>><mailto:bitrin...@gmail.com
<mailto:bitrin...@gmail.com>
 >>> <mailto:bitrin...@gmail.com <mailto:bitrin...@gmail.com>>>> wrote:
 >>>    Dear Experts,
 >>>    I am trying to find the band gap of a material (a supercell
of it)
 >>>    and I am getting the value 1.12 eV whereas the experimental
value of
 >>>    the same is 1.8 eV. Yes, DFT does underestimate the values
but it is
 >>>    too less! It should at least be close to 1.8 eV. So can you
please
 >>>    suggest ways to improve this value?
 >>>    I am using PBE-sol pseudopotentials.
 >>>    This is how my scf input file looks like:
 >>>    
 >>>   calculation = 'scf'
 >>>   etot_conv_thr =   1.35d-04
 >>>   forc_conv_thr =   1.00d-05
 >>>   outdir = './outdir'
 >>>   prefix = 'basic'
 >>>   pseudo_dir = './'
 >>>   tprnfor = .true.
 >>>   tstress = .true.
 >>>   verbosity = 'high'
 >>>    /
 >>>    
 >>>   degauss =   1.4699723600d-02
 >>>   ecutrho =   3.20d+02
 >>>   ecutwfc =   4.00d+01
 >>>   ibrav = 0
 >>>   nat = 135
 >>>   nosym = .false.
 >>>   ntyp = 3
 >>>   occupation

Re: [QE-users] How to improve the values calculated using QE?

[Nicola Marzari via users]

Blush :-)

nicola


On 11/11/2021 19:25, Stefano Baroni wrote:
Actually, at a closer look, and under any lighting, you are much more 
handsome than Brad Pitt. SB


On 11 Nov 2021, at 19:21, Nicola Marzari via users 
<mailto:users@lists.quantum-espresso.org>> wrote:




Dear Tarik,


DFT is not a theory that describes electronic excitations - there is 
only the total charge density in DFT, and it describes the ground state.


If you use Kohn-Sham DFT to approximate the kinetic energy functional 
introducing the non-interacting Kohn-Sham particles, these lead to 
band dispersions that look a bit like the quasiparticle excitations 
you are looking for.


Here, "look like" is in the same sense that I look like Brad Pitt, 
under proper lightning. A fleeting illusion, that can be occasionally 
oversold as a viable approximation. But 1.18 eV is what it is, at the end.


There is not much that we can do, a part from switching to theories 
and methods that describe electronic excitations.


Hope this helps,

nicola



On 11/11/2021 19:03, Tarik wrote:

Dear Experts,
Kindly go through my preceding mail and suggest ways to make the 
obtained values better. It is really important to me.

Thanking you,
Tarik
On Thu 11 Nov, 2021, 9:43 AM Tarik, <mailto:bitrin...@gmail.com><mailto:bitrin...@gmail.com 
<mailto:bitrin...@gmail.com>>> wrote:

   Dear Experts,
   I am trying to find the band gap of a material (a supercell of it)
   and I am getting the value 1.12 eV whereas the experimental value of
   the same is 1.8 eV. Yes, DFT does underestimate the values but it is
   too less! It should at least be close to 1.8 eV. So can you please
   suggest ways to improve this value?
   I am using PBE-sol pseudopotentials.
   This is how my scf input file looks like:
   
  calculation = 'scf'
  etot_conv_thr =   1.35d-04
  forc_conv_thr =   1.00d-05
  outdir = './outdir'
  prefix = 'basic'
  pseudo_dir = './'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
   /
   
  degauss =   1.4699723600d-02
  ecutrho =   3.20d+02
  ecutwfc =   4.00d+01
  ibrav = 0
  nat = 135
  nosym = .false.
  ntyp = 3
  occupations = 'smearing'
  smearing = 'cold'
   /
   
  conv_thr =   2.70d-08
  electron_maxstep = 80
  mixing_beta =   4.00d-01
   /
   ATOMIC_SPECIES
   Cs     132.9054519 cs_pbesol_v1.uspp.F.UPF
   I      126.90447 I.pbesol-n-kjpaw_psl.0.2.UPF
   Pb     207.2 Pb.pbesol-dn-kjpaw_psl.0.2.2.UPF
   ATOMIC_POSITIONS (crystal)
   Cs            0.166699        0.166699        0.166699
   Pb            0.00        0.00        0.00
   I             0.00        0.00        0.166699
   I             0.00        0.166699        0.00
   I             0.166699        0.00        0.00
   Cs            0.50        0.166699        0.166699
   Pb            0.01        0.00        0.00
   I             0.01        0.00        0.166699
   I             0.01        0.166699        0.00
   I             0.50        0.00        0.00
   Cs            0.833301        0.166699        0.166699
   Pb            0.99        0.00        0.00
   I             0.99        0.00        0.166699
   I             0.99        0.166699        0.00
   I             0.833301        0.00        0.00
   Cs            0.166699        0.50        0.166699
   Pb            0.00        0.01        0.00
   I             0.00        0.01        0.166699
   I             0.00        0.50        0.00
   I             0.166699        0.01        0.00
   Cs            0.50        0.50        0.166699
   Pb            0.01        0.01        0.00
   I             0.01        0.01        0.166699
   I             0.01        0.50        0.00
   I             0.50        0.01        0.00
   Cs            0.833301        0.50        0.166699
   Pb            0.99        0.01        0.00
   I             0.99        0.01        0.166699
   I             0.99        0.50        0.00
   I             0.833301        0.01        0.00
   Cs            0.166699        0.833301        0.166699
   Pb            0.00        0.99        0.00
   I             0.00        0.99        0.166699
   I             0.00     

Re: [QE-users] How to improve the values calculated using QE?

[Nicola Marzari via users]

Dear Tarik,


DFT is not a theory that describes electronic excitations - there is 
only the total charge density in DFT, and it describes the ground state.


If you use Kohn-Sham DFT to approximate the kinetic energy functional 
introducing the non-interacting Kohn-Sham particles, these lead to band 
dispersions that look a bit like the quasiparticle excitations you are 
looking for.


Here, "look like" is in the same sense that I look like Brad Pitt, under 
proper lightning. A fleeting illusion, that can be occasionally oversold 
as a viable approximation. But 1.18 eV is what it is, at the end.


There is not much that we can do, a part from switching to theories and 
methods that describe electronic excitations.


Hope this helps,

nicola



On 11/11/2021 19:03, Tarik wrote:

Dear Experts,

Kindly go through my preceding mail and suggest ways to make the 
obtained values better. It is really important to me.


Thanking you,
Tarik

On Thu 11 Nov, 2021, 9:43 AM Tarik, > wrote:


Dear Experts,

I am trying to find the band gap of a material (a supercell of it)
and I am getting the value 1.12 eV whereas the experimental value of
the same is 1.8 eV. Yes, DFT does underestimate the values but it is
too less! It should at least be close to 1.8 eV. So can you please
suggest ways to improve this value?

I am using PBE-sol pseudopotentials.

This is how my scf input file looks like:


   calculation = 'scf'
   etot_conv_thr =   1.35d-04
   forc_conv_thr =   1.00d-05
   outdir = './outdir'
   prefix = 'basic'
   pseudo_dir = './'
   tprnfor = .true.
   tstress = .true.
   verbosity = 'high'
/


   degauss =   1.4699723600d-02
   ecutrho =   3.20d+02
   ecutwfc =   4.00d+01
   ibrav = 0
   nat = 135
   nosym = .false.
   ntyp = 3
   occupations = 'smearing'
   smearing = 'cold'
/


   conv_thr =   2.70d-08
   electron_maxstep = 80
   mixing_beta =   4.00d-01
/

ATOMIC_SPECIES
Cs     132.9054519 cs_pbesol_v1.uspp.F.UPF
I      126.90447 I.pbesol-n-kjpaw_psl.0.2.UPF
Pb     207.2 Pb.pbesol-dn-kjpaw_psl.0.2.2.UPF

ATOMIC_POSITIONS (crystal)
Cs            0.166699        0.166699        0.166699
Pb            0.00        0.00        0.00
I             0.00        0.00        0.166699
I             0.00        0.166699        0.00
I             0.166699        0.00        0.00
Cs            0.50        0.166699        0.166699
Pb            0.01        0.00        0.00
I             0.01        0.00        0.166699
I             0.01        0.166699        0.00
I             0.50        0.00        0.00
Cs            0.833301        0.166699        0.166699
Pb            0.99        0.00        0.00
I             0.99        0.00        0.166699
I             0.99        0.166699        0.00
I             0.833301        0.00        0.00
Cs            0.166699        0.50        0.166699
Pb            0.00        0.01        0.00
I             0.00        0.01        0.166699
I             0.00        0.50        0.00
I             0.166699        0.01        0.00
Cs            0.50        0.50        0.166699
Pb            0.01        0.01        0.00
I             0.01        0.01        0.166699
I             0.01        0.50        0.00
I             0.50        0.01        0.00
Cs            0.833301        0.50        0.166699
Pb            0.99        0.01        0.00
I             0.99        0.01        0.166699
I             0.99        0.50        0.00
I             0.833301        0.01        0.00
Cs            0.166699        0.833301        0.166699
Pb            0.00        0.99        0.00
I             0.00        0.99        0.166699
I             0.00        0.833301        0.00
I             0.166699        0.99        0.00
Cs            0.50        0.833301        0.166699
Pb            0.01        0.99        0.00
I             0.01        

Re: [QE-users] [QE-developers] Inquiry: Quantum Espresso

[Nicola Marzari via users]

Dear Galina,


ENVIRON (http://www.quantum-environ.org) is a fairly comprehensive 
approach for Quantum ESPRESSO simulations in the presence of an implicit 
solvent and an electrolyte.


nicola


On 08/11/2021 18:53, Galina Galina wrote:

Dear Quantum Espresso,

Would you please let me know whether your package has a 3D-RISM-SCF 
module (freeware) that we would use for quantum chemistry calculations 
of CO2+H2 reduction reaction on nanocatalysts in dense solvent / solutions?

If not, are you planning to implement it in the near future?

Thank you,

Galina

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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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[QE-users] Two posdoctoral openings - Wannier/Hubbard/Koopmans

[Nicola Marzari via users]

Dear QE forum,


in case someone is interested, we have two openings for postdoctoral 
positions in code/method development, for Wannier-based Hubbard and 
Koopmans functionals to run on accelerated architectures - so very 
suited for people with a methodological and parallel/C++ coding slant.


The full ad is here below, and the deadline is Oct 31:
https://psi-k.net/jobs/epfl-theos-marzari-two-postdoctoral-position-on-s/

Many thanks for your attention,


nicola


--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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Re: [QE-users] Atomic velocities units

[Nicola Marzari via users]

On 10/08/2021 11:39, Lorenzo Paulatto wrote:
The velocities are both printed in any place, but it is not the first 
time I get this request, maybe it could be added in the future. That 
said, they are trivial to compute v(t)=(r(t-1)-r(t))/dt


--
Lorenzo Paulatto


quick one - maybe better as v(t)=(r(t+1)-r(t-1))/(2 dt) (note also the sign)

nicola



--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, SNSF
Head, Laboratory for Materials Simulations, Paul Scherrer Institut
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact
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[QE-users] review on electronic-structure methods and computational materials design

[Nicola Marzari via users]

Dear QE users,


with Andrea Ferretti and Chris Wolverton we have written a review for 
Nature Materials on electronic-structure methods that is out today:


https://www.nature.com/articles/s41563-021-01013-3

We are also allowed to distribute an open access, view-only version:

https://rdcu.be/clrH2

There are many QE examples and applications, and we hope it could be a 
useful reading to gain a broad perspective on materials simulations from 
first-principles.


Also in the same issue there is a Perspective by Steve Louie, and other 
reviews at larger scales or on machine learning (it's an "Insight" on 
Computational Materials Design):


https://www.nature.com/collections/dhcfgffecf

Any comments or corrections (directly to me) also very welcome!


nicola


--
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Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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Re: [QE-users] under pressure PbTaSe2 vc-relax calculation

[Nicola Marzari via users]

Dear all,


1) a perennial recommendation of mine is indeed to make sure the cutoffs 
for wfcs and rho are both enough to have the stress well converged - 
this was one key critiations for the SSSP (that you can find here 
https://www.materialscloud.org/discover/sssp/). Reasonably tuned 
parameters and appropriate pseudopotentials for any input structure can 
be obtained from here:

https://www.materialscloud.org/work/tools/qeinputgenerator

Your mileage might vary, and you might be able to get away with looser 
thresholds, or need tighter ones, but that is a recommended starting 
point, to understand what you need.


2) a second recommendaiton in dealing with solids is to use PBEsol 
rather than PBE as a first default choice.


As always, test crtically these input parameters to understand how they 
are affecting your calculations.


nicola


On 26/05/2021 10:28, Stefano de Gironcoli wrote:
more than with a different set of k-points, the last scf  is done 
resetting the spherical cutoff according to the last cell (during the 
vc-relaxation the G vectors in the list are deformed but the miller 
indices included in the list are not updated and the sphere actually 
deforms into an ellipsoid ).


As the pressure converges slowly with cutoff if the pressure changes 
significantly this is an indication that the cutoff might have been too 
low or that  the cell has changed a lot.


stefano

On 26/05/21 09:40, mkondrin wrote:

Dear Rencong,

I believe that the last step in vc-relax calculations is made in 
slightly different Brillouin zone (calculated in relaxed variable cell 
parameters), so the pressure calculated in the last step may be 
different from whose obtained in the previous step (where Brillouin 
zone of the original cell was used convergence criteria with desired 
pressure is checked).


It also seems to me that your pressure is rather small. May be it has 
sense to increase the pressure to at least 10 kbar.


Sincerely yours,
M. V. Kondrin


On 26.05.2021 05:48, 连云龙 wrote:

Dear Rencong,

I had similar experiences when I use QE pw.x to relax structures 
under pressure and I want to follow this conversation.


My experience is that, the behaviour and result of relaxation depend 
largely on the pesudopotential.


It is also helpful to investigate the energy and pressure during the 
relaxation.


In order for other experts to help you, could you please provide:
(1) the pseudopotentials used in the calculation
(2) the entire output file of pw.x, or at least the section contains 
the final coordinates? (search "End of BFGS" in the output file)

(3) your name and affiliation (this is the rule of the mailing list)

Best,
Yunlong



--
Yunlong LIAN ORCID : https://orcid.org/-0002-9474-2181 CSNS, 
Dongguan Neutron Science Center Dongguan, Guangdong, P. R. China 连云 
龙 中国散裂中子源 中子科学部 A1-629 (内线 303) 中国广东省东莞市

-Original Messages-
From:Amadeus <760158...@qq.com>
Sent Time:2021-05-25 15:22:02 (Tuesday)
To: users 
Cc:
Subject: [QE-users] under pressure PbTaSe2 vc-relax calculation


Dear QE developer


I did the structural relaxation calculation for Pb at pressure of 
3kbar， this is relax.in




   prefix='PbTaSe2',
   calculation='vc-relax', pseudo_dir='../../', outdir='./tmp', 
verbosity='high',

   tprnfor=.true., tstress=.true., forc_conv_thr=1.0d-4, nstep=100,
/

   ibrav= 0, nat= 4, ntyp= 3,
   occupations = 'smearing', smearing = 'gauss', degauss = 1.0d-2,
   ecutwfc = 50, ecutrho = 500,
/

   conv_thr = 1.0d-8
   mixing_beta = 0.7d0
/

/

   cell_dynamics  = "bfgs"
   press  =  2.7e+00
   press_conv_thr =0.1
/
ATOMIC_SPECIES
   Ta 180.9479 Ta.UPF
   Pb 207.2 Pb.UPF
   Se 78.96 Se.UPF
CELL_PARAMETERS (angstrom)
    3.483470  0.00  0.00
   -1.741735  3.0167735133  0.00
    0.00  0.00  9.475530
ATOMIC_POSITIONS (crystal)
   Pb  0.00  0.00  0.00
   Se  0.00  0.00  0.324671
   Ta  0.33  0.67  0.50
   Se  0.00  0.00  0.675329
K_POINTS {automatic}
   15 15 5 0 0 0


In relax.in, press=3.0kbar. But after pw.x is done, relax.out show 
that total stress  (Ry/bohr**3)  (kbar) P=-0.83, and This is 
inconsistent with press=3. this is part of relax.out



[rencong@mu01 phonon]$ grep 'Computing stress (Cartesian axis) and 
pressure' -A 15 relax.out






  Computing stress (Cartesian axis) and pressure


   total   stress  (Ry/bohr**3) (kbar) P=    2.93
    0.2030  -0.   0.    2.99 -0.00 0.00
   -0.   0.2030  -0.   -0.00 2.99 -0.00
   -0.   0.   0.1921   -0.00 0.00 2.83


  kinetic stress (kbar)  26877.23  0.00  0.00
 0.00  26877.23 -0.00
 0.00  0.00  26796.57


  local   stress (kbar)-103340.53  0.03  0.00
   

Re: [QE-users] Query about density of states calculations for crystalline and amorphous supercells

[Nicola Marzari via users]

Mostly yes - e.g. look at the work of Pasquarello's group (and many 
others, of course) on the topic - many menaningful papers in the past 20 
years.

nicola


On 20/05/2021 18:41, alex davila wrote:

Dear all,

I am interested in learning if QE is suitable for DOS calculations of 
crystalline and amorphous supercells.


In the case of c-Si supercell of 216 atoms, after scf, nscf, and dos 
calculations, my DOS output is calculated without taking into account 
the nscf results that fail: I've tried these calculations given 
different paths for the K_POINTS at the correspondent BZ of the supercell.


In the case of an a-Si supercell, I wonder if calculations with PW may 
produce a right DOS output or other implementations would be needed.


Any advice will be appreciated.

Regards,

Alex
Materials Science and Renewable Energies Group (MatER-PUCP)
Department of Sciences
Pontifical Catholic University of Peru

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Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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[QE-users] postdoctoral (or PhD) positions on spectroscopies with Quantum ESPRESSO and ENVIRON

[Nicola Marzari via users]

Dear Quantum ESPRESSO users,


in case some of you are interested, we have two postdoctoral openings in 
the group, to develop first-principles spectroscopies using Quantum 
ESPRESSO and the electrochemical libraries of ENVIRON. All details at

http://theossrv1.epfl.ch/uploads/Main/Openings/EPFL-THEOS-Operando.pdf

These would also be suitable to an experienced student wanting to pursue 
a PhD in the field.


nicola



--
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Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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