Re: [QE-users] Doubt regarding choice of conv_thr

[Nicola Marzari via users]

Yes, one should take into account the number of ions or electrons - a 
good starting point for a given system is given by the QE Input 
generator (soon to be updated with our latest refined protocols):


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

nicola


On 19/09/2024 17:09, Vinay Maithani wrote:

Dear Quantum Espresso community,

How to select an appropriate*etot_conv_thr* and *conv_thr* given that 
these are extensive quantities?


Since etot_conv_thr represents the total energy convergence threshold 
for ionic minimization and is extensive, does this value depend on the 
system size? Should we scale it according to the system size, or can a 
fixed threshold (e.g., 1.0D-4) be used consistently for both small and 
large systems? *How does one decide on the appropriate convergence 
criteria*, and will it differ based on system complexity?

Can we use thresholds for these quantities arbitrarily very small or large?

Thank you for your time and guidance.
--
Regards,
Vinay Maithani
MME, IIT Kharagpur

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--
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Re: [QE-users] Error during dielectric constant calculation with epsilon.x

[Nicola Marzari via users]

d peaceful scientific, cultural,
and economic cooperation amongst peoples
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Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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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 
<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 <http://www.rse-web.it>
<https://it.linkedin.com/company/ricerca-sul-sistema-energetico---rse-spa> 
<https://twitter.com/rsenergetico> <https://www.youtube.com/user/RSEmedia>


P Per la tutela dell'ambiente, prima di stampare questa e-mail pensa 
bene se è veramente necessario





RSE SpA ha adottato il Modello Organizzativo ai sensi del
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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] 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




----------
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] 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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--
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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] 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&hl=en&user=YjHKNAUJ&cstart=20&pagesize=80&sortby=pubdate&citation_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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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] 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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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] 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 
<https://www.materialscloud.org/discover/sssp/table/efficiency>


Materials Cloud

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


<https://www.materialscloud.org/discover/sssp/table/efficiency>

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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--
Dr. Lorenzo Paulatto
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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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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--
------
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] 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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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] 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 <http://people.epfl.ch/265334>



*From:*users <mailto:users-boun...@lists.quantum-espresso.org>> 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 
<mailto: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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--
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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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------
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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] 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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--
--
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 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
Contact info and websites at http://theossrv1.epfl.ch/Main/Contact

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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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> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> ___
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Re: [QE-users] 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

Sent from a tiny keyboard... Contact info:
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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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> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
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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 
<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 <https://fhrc.huji.ac.il/people/leeor-kronik>(Weizmann 
Institute of Science, Israel)


Renata Wentzcovitch 
<https://www.apam.columbia.edu/faculty/renata-wentzcovitch>(Columbia 
University, USA)


Matteo Gatti <https://etsf.polytechnique.fr/People/Matteo>(École 
Polytechnique, France)


*
*

Lecturers:

*

**

*

Nicola Marzari <https://people.epfl.ch/nicola.marzari>(EPFL and PSI, 
Switzerland)


Giovanni Pizzi <https://people.epfl.ch/giovanni.pizzi>(EPFL and PSI, 
Switzerland)


Edward Linscott <https://people.epfl.ch/edward.linscott>(EPFL, Switzerland)

Iurii Timrov <https://people.epfl.ch/iurii.timrov>(EPFL, Switzerland)

Nicola Colonna <https://www.psi.ch/en/lns/people/nicola-colonna>(PSI, 
Switzerland)


Andrea Floris <https://staff.lincoln.ac.uk/afloris>(Lincoln University, UK)

Andrea Ferretti <http://max-centre.eu/andrea-ferretti-0>(CNR Modena, Italy)

***
**

**Matteo Cococcioni 
<https://fisica.unipv.it/personale/Persona.php?ID=505>(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:
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> 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
>>> ___
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>>> users mailing list users@lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
> 
> 
> 
> 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,
> and economic cooperation amongst peoples
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] 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&co 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
___
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
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Re: [QE-users] Slow convergence

[Nicola Marzari via users]

33
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 0.03623 0.49359
O 0.46397 0.939 0.00552
O 0.53603 0.061 0.00552
O 0.52684 0.83629 0.49854
O 0.47316 0.16371 0.49854
O 0.3369 0.9734 0.00109
O 0.6631 0.0266 0.00109
O 0.96597 0.8783 0.49454
O 0.03403 0.1217 0.49454
O 0.36959 0.53688 0.00851
O 0.63041 0.46312 0.00851
O 0.41584 0.45689 0.50345
O 0.58416 0.54311 0.50345
O 0.95097 0.08093 0.00343
O 0.04903 0.91907 0.00343
O 0.88249 0.82729 0.99949
O 0.11751 0.17271 0.99949
O 0.32643 0.61647 0.49726
O 0.67357 0.38353 0.49726
O 0.29094 0.492 0.49589
O 0.70906 0.508 0.49589
O 0.99061 0.20902 0.00312
O 0.00939 0.79098 0.00312
O 0.78502 0.77115 0.49848
O 0.21498 0.22885 0.49848
O 0.27143 0.71412 0.99854
O 0.72857 0.28588 0.99854
O 0.25631 0.36378 0.49729
O 0.74369 0.63622 0.49729
O 0.86389 0.24402 0.0024
O 0.13611 0.75598 0.0024
O 0.19451 0.43577 0.99433
O 0.80549 0.56423 0.99433
O 0.93555 0.30655 0.50484
O 0.06445 0.69345 0.50484
O 0.15356 0.29887 0.99582
O 0.84644 0.70113 0.99582
O 0.79982 0.34627 0.50333
O 0.20017 0.65373 0.50333
O 0.1236 0.39265 0.4933
O 0.8764 0.60735 0.4933
O 0.89318 0.37688 0.00597
O 0.10682 0.62312 0.00597
O 0.0611 0.46377 0.99359
O 0.9389 0.53623 0.99359
O 0.96397 0.439 0.50552
O 0.03603 0.561 0.50552
O 0.02684 0.33629 0.99854
O 0.97316 0.66371 0.99854
O 0.8369 0.4734 0.50109
O 0.1631 0.5266 0.50109
W 0.5 0 0.74844
W 0.87802 0.03479 0.0398
W 0.12198 0.96521 0.0398
W 0 0.5 0.24844
W 0.37802 0.53479 0.5398
W 0.62198 0.46521 0.5398
CELL_PARAMETERS (alat)
20.981701    0.00     0.00
  0.0175589792   20.9607926454     0.00
  0.00    0.00     3.823210
K_POINTS {automatic}
  1 1 5 0 0 0
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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]

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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


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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) 
<http://theossrv1.epfl.ch/Main/Pseudopotentials>), 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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------
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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] 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
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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] 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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------
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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





--
------
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,


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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----------
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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] 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:
 >>>    &CONTROL
 >>>   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'
 >>>    /
 >>>    &SYSTEM
 >>>   degauss =   1.4699723600d-02
 >>>   ecutrho =   3.20d+02
 >>>   ecutwfc =   4.00d+01
 >>>   ibrav = 0
 >>>   nat = 135
 >>&g

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

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

[Nicola Marzari via users]

Pb            0.00        0.01        0.99
I             0.00        0.01        0.833301
I             0.00        0.50        0.99
I             0.166699        0.01        0.99
Cs            0.50        0.50        0.833301
Pb            0.01        0.01        0.99
I             0.01        0.01        0.833301
I             0.01        0.50        0.99
I             0.50        0.01        0.99
Cs            0.833301        0.50        0.833301
Pb            0.99        0.01        0.99
I             0.99        0.01        0.833301
I             0.99        0.50        0.99
I             0.833301        0.01        0.99
Cs            0.166699        0.833301        0.833301
Pb            0.00        0.99        0.99
I             0.00        0.99        0.833301
I             0.00        0.833301        0.99
I             0.166699        0.99        0.99
Cs            0.50        0.833301        0.833301
Pb            0.01        0.99        0.99
I             0.01        0.99        0.833301
I             0.01        0.833301        0.99
I             0.50        0.99        0.99
Cs            0.833301        0.833301        0.833301
Pb            0.99        0.99        0.99
I             0.99        0.99        0.833301
I             0.99        0.833301        0.99
I             0.833301        0.99        0.99

CELL_PARAMETERS (angstrom)
   18.712038000   0.0   0.0
    0.0  18.712038000   0.0
    0.0   0.0  18.712038000

K_POINTS automatic
5 5 5 0 0 0


Thanking you,
Tarik
IIT Indore


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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] [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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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


--
--
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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] 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



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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


------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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]

    0.00  26877.23 -0.00
 0.00  0.00  26796.57


  local   stress (kbar)-103340.53  0.03  0.00
 0.03-103340.50  0.00
 0.00  0.00  89394.48


  nonloc. stress (kbar)   7797.15  0.00  0.00
--
  Computing stress (Cartesian axis) and pressure


   total   stress  (Ry/bohr**3) (kbar) P=    2.96
    0.2009  -0.   0.    2.96 -0.00 0.00
   -0.   0.2009  -0.   -0.00 2.96 -0.00
    0.  -0.   0.2028    0.00 -0.00 2.98


  kinetic stress (kbar)  26879.49  0.00  0.00
 0.00  26879.49 -0.00
 0.00 -0.00  26798.86


  local   stress (kbar)-103299.75  0.03  0.00
 0.03-103299.72  0.00
 0.00  0.00  89348.84


  nonloc. stress (kbar)   7797.79 -0.00  0.00
--
  Computing stress (Cartesian axis) and pressure


   total   stress  (Ry/bohr**3) (kbar) P=   -0.83
   -0.0653  -0.  -0.   -0.96 -0.00 -0.00
    0.  -0.0653   0.    0.00 -0.96 0.00
    0.   0.  -0.0384    0.00 0.00 -0.56


  kinetic stress (kbar)  26883.07  0.00 -0.00
 0.00  26883.07 -0.00
    -0.00 -0.00  26802.38


  local   stress (kbar)-103303.36  0.03  0.00
 0.03-103303.33  0.00
 0.00  0.00  89345.22


  nonloc. stress (kbar)   7795.83 -0.00  0.00


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http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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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
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[QE-users] Vanderbilt and Resta online lectures - CECAM-MARVEL "Classics in molecular and materials modelling"

[Nicola Marzari]

Dear all,


this might be of interest to many of you - David Vanderbilt and Raffaele 
Resta will present two online live talks and an interview on "Berry 
phases in condensed matter physics", on Mar 23 2021, at 3pm Central 
European Time (for those in the US, note that the country will be on 
summer time then, while Europe is still on winter time).


Happy viewing,

            nicola marzari


   CECAM-MARVEL "Classics in molecular and materials modelling"

In this series, organized jointly by CECAM <https://www.cecam.org/> 
(Centre Européen de Calcul Atomique et Moléculaire) and the MARVEL 
<https://nccr-marvel.ch/> Center on Computational Design and Discovery 
of Novel Materials, methods that have become fundamental tools in 
computational physics and chemistry will be presented by their 
originators at a level appropriate for master and graduate students. The 
lectures will be followed by an interview with the presenters: we’ll ask 
them to recall for us the period, problems, people and circumstances 
that accompanied the creation of milestone methods and algorithms that 
we now routinely use.


We hope that you will be able to join us and share with us this unusual 
and interesting opportunity to learn first hand from pioneers who have 
contributed significantly to our field and to get to know better the 
history and anecdotes behind work that is now recorded in books.


*David Vanderbilt* (Rutgers University) & *Raffaele Resta* (IOM-CNR 
Democritos, Trieste):

/Berry phases in condensed matter physics
/March 23, 2021 – 15:00-17:45 (CET) [at this date, this is 10:00 EDT or 
07:00 PDT]


https://epfl.zoom.us/j/83512387218 <https://epfl.zoom.us/j/83512387218> 
  Passcode: 4628


15:00–Introduction
15:10–Conceptual Aspects of the Theory of Electric Polarization and 
Orbital Magnetization (D. Vanderbilt)

16:00–Break
16:10–Electric Polarization, Orbital Magnetization, and Other 
Geometrical Observables (R. Resta)

17:00–Interview and recollections
17:45–End

Abstracts and details 
<https://nccr-marvel.ch/events/classics-resta-vanderbilt>


Mark your calendars for the following event:

*Daan Frenkel* (University of Cambridge) & *Tony Ladd* (University of 
Florida)
May 20, 2021 – 15:00-17:45 (CEST) [at this date, this is 09:00 EDT or 
06:00 PDT]


Details will be announced here 
<https://nccr-marvel.ch/events/classics-frenkel-ladd>


http://psi-k.net/events/cecam-marvel-classics-in-molecular-and-mate 
<http://psi-k.net/events/cecam-marvel-classics-in-molecular-and-mate>



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Re: [QE-users] Appropriate wavefunction cutoff

[Nicola Marzari]

Also, find your pseudos here and get a reliable estimate:
https://www.materialscloud.org/discover/sssp/


                nicola


On 11/02/2021 10:34, SOUMYAKANTA PANDA via users wrote:

Dear Hadibandhu Moharana
First try to converge the ground state energy by relaxing your system 
by varying the cutoff energy. Then you can easily find your required 
cutoff energy.


Best Regards,
Soumyakanta Panda
Research Scholar
Nano Magnetism and Magnetic Materials Laboratory
IIT Bhubaneswar


On Thu, Feb 11, 2021 at 9:45 AM Hadibandhu Moharana 
mailto:moharanahadiband...@gmail.com>> 
wrote:


Hello,
           I am trying to study a system consisting of Li,Cl and
O. I am using pseudopotentials of PAW(pbe) type for Li,Cl and O
with suggest minimum wavefunction cutoffs 78Ry, 36Ry and 47Ry
respectively.
          From the literatures , it is clear that everyone is
using cutoff less than 50Ry, but I found that total energy is
conserved for a cutoff of 80Ry from scf calculations.
           In this case, what cutoff should I use?


Thanks
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Re: [QE-users] oxidation state of the Mn-atom

[Nicola Marzari]

some references that might help

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.108.166403

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.10.041031

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b00281



On 09/02/2021 19:59, Offermans Willem wrote:

Hi Oukahou and Quantum Espresso friends,


If you look for a method to give you the oxidation state you want, then
I would stop looking and take the oxidation state you want.

However, if a method gives you a certain oxidation state, then this is
the oxidation state you obtained under certain conditions and applying a
certain methodology. If you don’t feel comfortable with the obtained value
and you have reasonable doubts about the methodology
or conditions (parameters), you should focus on the latter. If you need
help with this, you should disclose the methodology and/or the
parameters to us and discuss what you think might be wrong or
needs reconsideration.

I’m pretty certain that someone wants to help you out or give you advice.
With the information at hand, it will be very difficult.


Met vriendelijke groeten,
Mit freundlichen Grüßen,
With kind regards,


Willem Offermans
Researcher Electrocatalysis SCT
VITO NV | Boeretang 200 | 2400 Mol
Phone:+32(0)14335263 Mobile:+32(0)492182073

willem.offerm...@vito.be 


On 9 Feb 2021, at 17:45, OUKAHOU SAID > wrote:


Hello QE-users,
I am working on lithium ion batteries specially on cathode materials. 
For instance, I am doing a simulation on the active material LiMnPO4, 
and I want to calculate the oxidation state of the Mn-atom in 
LiMnPO4. I would be grateful if anyone  can help to figure out the 
oxidation state of the Mn-atom. I have used bader charge analysis for 
LiMnPO4. however it doesn't give me  the oxidation state that i want.

thank you in advance.


---
Best regards,

Oukahou said
*
/PhD Student
/
/Laboratoire des sciences des Matériaux, des Milieux et de la 
Modélisation (LS3M)/

/Faculté Polydisciplinaire de Khouribga
/
/Université Sultan Moulay Slimane
/
/Béni Mellal , Maroc/


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Re: [QE-users] "Re2: Convergence Issues?"

[Nicola Marzari]

Dear Stefano, Lucas,

this is one of the few areas where I disagree with Stefano - I think we 
should use the free energy (forces and stresses are the total derivative 
of the free energy, not the internal energy), and that level-crossing 
instabilities are exceedinfly difficult to cure with iterative 
algorithms (my own opinions are here: 
http://theossrv1.epfl.ch/Main/ElectronicTemperature),



            nicola


On 25/01/2021 16:33, Stefano Baroni wrote:
I beg to slight differ. It does not make much sense to assign a 
“default value” to the Gaussian smearing, unless one makes sure that 
the computations are well converged with respect to the number of k 
points, for that specific value of the smearing. The rational 
procedure to follow is: 1) start with whatever value of the smearing 
one wishes, and make sure that the (internal, *not* “fake free”) 
energy is well converged with respect to the number of k points. If 
the number of k points is sufficient, it is likely that no nasty 
oscillation would arise; 2) decrease the smearing and vary the number 
of k points accordingly. HTH — Stefano B



—
Stefano Baroni -  SISSA, Trieste - http://stefano.baroni.me 
, stefanobaroni (skype)


I do not mind if you think slowly, but I do object when you publish 
more quickly than you think [W.E. Pauli to an unknown colleague, as 
reported by N. Kemmer]


On 25 Jan 2021, at 15:08, Lucas Nicolás Lodeiro Moraga 
mailto:lucas.lode...@ug.uchile.cl>> wrote:


Hi,
It appears a metallic oscillation, where a couple or more states 
change their relative energy, and change their energetical order, 
then the occupation changes abruptly (non continuous). If this is the 
problem, it is better to increase the degauss value and/or change the 
smearing method.
Typically I use methfessel-paxton with 0.015 Ry for degauss, which 
mimics the VASP default values. When you get a converged system, you 
can try to decrease (slowly) the degauss.


Regards - Lucas Lodeiro
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Re: [QE-users] mechanical stability under pressure from phonons

[Nicola Marzari]

I think what Grimvall is saying is that there has been no rigorous 
discussion before, but in their review they make this discussion, and 
show how the stability condition for phonons does not need any 
correction - the material collapses at the pressure where the phonon 
dispersions calculated at the corresponding volume go negative. Anyhow, 
they cite a few papers and their follow-up corrections.


nic


On 11/01/2021 11:04, Uri Argaman wrote:

Hi all
In the literature the mechanical stability condition using elastic 
constants includes explicitly the pressure:

In cubic symmetry, for example:
C11 + 2*C12 +P>0;
C44 +P>0;
C11 + C12 + 2*P>0;
from: Grimvall et al. REVIEWS OF MODERN PHYSICS, VOLUME 84,  2012
In this paper, they write: " There seems to be no rigorous discussion 
of this point in papers that have presented ab initio calculations of 
phonon dispersion curves under pressure,..."
The stability condition from phonons: omega>0 for all modes. It seems 
that it is not equivalent, because the phonon condition is at 
constant volume. Is it known what is the condition at constant pressure?

Than you very much
Uri Argaman
Ben-Gurion University of the Negev
Israel

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Re: [QE-users] Replace vacuum with virtual environment of different permittivity

[Nicola Marzari]

Dear Rakesh,

the ENVIRON libraray can do that:
http://www.quantum-environ.org

Note that interesting and important effects could come from the 
interface states of the perovskites, though, and so a continuum model 
might not be enough - it also depends if you care about the interface 
with a liquid, or with a solid.


  nicola

On 26/12/2020 16:12, Rakesh Pradhan wrote:

Dear All,

I am currently studying perovskite interfaces. I want to replace the 
vacuum of my simulation cell with materials of different permittivity 
and calculate their density of states. I'm aware that this can be 
achieved by creating interfaces of different materials with 
perovskites, however, my perovskite system is very large and I want to 
avoid additional atoms.


Is there any code which can replace the vacuum with a 
virtual material of different permittivity?


--
THANKS & REGARDS
*
*
*Rakesh Rosan Pradhan*
*PhD Scholar*
*Applied Physics*
*King Abdullah University of Science & Technology (KAUST)*


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 
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Re: [QE-users] Segmentation fault when using ph.x, MacOSX

[Nicola Marzari]

You could also try and run it from inside the Quantum Mobile - that's an 
ubuntu virtual machine that you can load on your Max:


https://quantum-mobile.readthedocs.io/en/latest/index.html

                nicola


On 13/12/2020 12:06, Paolo Giannozzi wrote:
If it crashes when function "zdotc" is called, it is the usual problem 
with complex functions, explained in the user guide. The only real 
solution is to replace all calls to zdotc with an equivalent call to 
fortran intrinsic dot_product.


Paolo

On Sun, Dec 13, 2020 at 1:40 AM Сергей Клявинек > wrote:


Hello everyone!
I ran into a problem - I can't use ph.x  package. When I try to
run the script, I get a segmentation fault, regardless of the
folder I am trying to save the output to. I ran the calculations
using this manual:
http://www.fisica.uniud.it/%7Egiannozz/QE-Tutorial/handson_phon.html

in-file - si.phG.in 
I read that this happens on MacOS, but I couldn't find a solution.
Maybe someone knows how to determine exactly where the error is
and how to fix it?
Best regards,
Sergei Kliavinek
CSE EPFL
JIHT RAS
DMCP MIPT





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


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Re: [QE-users] convergence problem

[Nicola Marzari]

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

and reducing the mixing

On 30/11/2020 21:42, Sohail Ahmad via users wrote:

Dear QE users,
Please have a look at the scf file and suggest measures so as it could get 
converge

&control
   calculation = 'scf',
   restart_mode = 'from_scratch',
   prefix = 'NiCrSi',
   pseudo_dir = '/home/sohail/pseudo',
   outdir = './OUT',
/
&system
  ibrav = 2, a = 19.4833805946, b = 19.4833805946, c = 19.4833805946, cosAB = 
0.0, cosBC = 0.0, cosAC = 0.0,
   nat = 3, ntyp = 3,
   ecutwfc = 75,
   ecutrho = 300,
   nbnd = 25,
   occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
/
&electrons
   mixing_beta = 0.3,
   conv_thr = 1.0d-9,
   electron_maxstep = 999,
/
ATOMIC_SPECIES
Cr  51.99  Cr.pbe-sp-van.UPF
Si  28.08  Si.pbe-n-van.UPF
Ni  58.69  Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS  {alat}
Cr   0.  0.  0.
Si   0.5000  0.5000  0.5000
Ni   0.2500  0.2500  0.2500
K_POINTS AUTOMATIC
16 16 16 0 0 0




-

Sohail Ahmad

Department of Physics

King Khalid University

Saudi Arabia



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Re: [QE-users] Optimal QE setup for molecular crystals (pseudopotentials, k-space campling, performance) ..

[Nicola Marzari]

Dear all,

the comparisons that Andrii mentions are all done here below, and very 
comprehensively - so it's just a matter of studying those and 
understanding them (it's not rocket science, and most of you are rocket 
scientists): https://www.materialscloud.org/discover/sssp/


I'll keep repeating this above forever, inspired by Cato the Censor.

Also, for lanthanides (a different post), you should be extremely 
careful - the ones I would trust are the Topsakal Wentzcovitch ones.


Nicola

On 17/11/2020 12:52, Andrii Shyichuk via users wrote:

Dear Mihal,

A few suggestions:
1). Compare a few types of PPs: PSLibrary (QE defaults), GBRV 
(https://www.physics.rutgers.edu/gbrv/), ATOMPAW 
(http://users.wfu.edu/natalie/papers/pwpaw/PAWDatasets.html).


2). The cutoff depends on the PPs, I'd not go below the value 
recommended for the PPs used.


3). Are there any compounds chemically similar to yours, with good 
known structures?
If not - cell dimension is at least some quality indicator, good 
dimensions mean good bond lengths, approximately.
Smooth EOS (energy-volume curve) is an indicator that your setup is 
self-consistent (basis is good, etc).


4). Gamma-only is not good for geometries. I'd use 3x3x3 grid (if your 
systems is approximately a cube), or 2x2x2 (yes, K_POINTS automatic  2 
2 2 0 0 0 ) if 3x3x3 is too much.


Best regards.
Andrii Shyichuk, University of Wrocław


W dniu 2020-11-16 22:46, Husak Michal napisał:

Hi all ...


Before I continue I would like to mentioned I had done the homework on
this topic (checked mail list, studied about 20 related articles, done
a few hundred test calculations by QE and CASTEP) ...

The target of my work is to verify (enhance quality) of X-ray based
molecular crystal structure solution

by DFT methods ...


Target molecules:  primary C,H,N,O composed middle size molecular
crystals (100-500 atoms per unit cell).

Insulators. Non magnetic. Other atoms potentially: F,Cl,S,B,Na,


Goal: Confirm the geometry from X-ray is correct (by results RMS
comparison with original) ..


Questions:

1) What pseudopotential is suitable ? pbe-n-rrkjus_psl.1.0.0.UPF Like 
one ?



2) Some sources suggest 38 Ry cutf off (study done in VASP),
H-ultrasoft potential suggest 46 Ry cutoff,

QE related study (M. Lund) suggest 55 Ry cut off ...

I need to screen a lot of structures = be fast = low cut off . Opinion ?


3) How can i determine I had chosen correct parameters ?

Comparison of RMS with X-ray data is not reliable - X-ray shows
position of max. electron density,

DFT shows positions of cores (especially for H-atoms)  ...

Any idea how to benchmark, before doing some large screening ?

Does exist some database of "100% reliable determined" reference 
structures ?



4) Gamma K-point only usage will be nice.

M. Lund work suggest 2x2x2 k-point to be OK  (is it identical to
K_POINTS automatic  2 2 2 0 0 0 ) ?

What do you thing ?


Thanks for any ideas


Michal Husak


UCT Prague
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Re: [QE-users] Pw.x doesn't progress in supercell calculation

[Nicola Marzari]

On 17/11/2020 09:37, Riki Suemasa wrote:

Dear all,



make a 1x1x1 cell. does it work? yes/no. 2x2x1? yes/no. 3x3x1? yes/no


            nic


I'm trying 4x4x1 supercell slab calculation using attached inputfile.
Pw.x doesn't make errors but output file doesn't progerss.
I think this is caused by some basic issues...(nat, or k-point setting 
in supercell ?) but I didn't find answer.

I tried to reduce the number of atoms, but it didn't work.

I would appreciate if you reply.

Riki

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Re: [QE-users] CASTEP to QE setup parameters conversions

[Nicola Marzari]

On 15/11/2020 21:26, Paolo Giannozzi wrote:


CASTEP uses norm-conserving pseudopotentials only, if I remember 
correctly, so the cutoff on the charge density (ecutrho) can be set to 
ecutrho=4*ecutwfc.



Not very improtant for QE, but for the record they have ultrasoft - 
Chris Pickard coded those in the late '90s, and they are the default:


http://www.castep.org/CASTEP/FAQPseudopotentials

nicola


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Re: [QE-users] CASTEP to QE setup parameters conversions

[Nicola Marzari]

One possibility would be to upload your structure (or in principle even 
your CASTEP .cell file) here:

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

This will give you fairly reliable input parameters (cutoff, sampling, 
etc...) and pseudopotentials for a scf calculation,

and then try to understand from this document
https://www.quantum-espresso.org/Doc/INPUT_PW.html
what else you need

            nicola


On 14/11/2020 20:13, Husak Michal wrote:

Hi all


I was working a lot with CASTEP last years ...

I want to switch some my projects to  QE + do head to head comparison with 
CASTEP.

I am confused by some selected corresponding setup parameters conversion

(I had handled the rest including input formats conversion myself):


QE: etot_conv_thr  (a.u.]

CASTEP: geom_energy_tol (eV/atom)

Should I simply  recalculate eV to a.u. and multiply by number of atoms in unit 
cell ?

Why the definition in QE/CASTEP differs ?


QE: forc_conv_thr  (a.u.)

CASTEP: geom_force_tol (eV/angstrem)

I have no idea how to convert this  parameter 


QE: non existing criteria

CASTEP: geom_disp_tol (angstrem) , Maximal atom displacement during a cycle ..

Sound like QE does not check this criteria ?


QE: ecutrho (Ry), default 4 * ecutwfc

CASTEP: non existing parameter

Any idea why CASTEP does not use this parameter ?


QE: conv_thr  , units not found/missing in manual, probably (a.u.) ?

CASTEP: elec_energy_tol (eV/atom)

Should I simply  recalculate eV to a.u. and multiply by number of atoms in unit 
cell ?

Why the definition differs ?


Michal Husak

UCT Prague, Department of Solid State Chemistry




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[QE-users] Tue Nov 17, 3pm CET: Prof. Stefano Baroni, MARVEL Distinguished Lecture

[Nicola Marzari]

Dear espressionists,


I wanted to mention that our own Stefano Baroni will deliver on Tuesday 
(Nov 17, 3pm CET) a MARVEL Distnguished Lecture on their recent 
achievements in transport theories. The lecture is in live streaming, 
open to anyone, and followed by a public Q&A. You are all very much 
welcome to attend.


Here are the tile and zoom link (do not forget the passcode!), with a 
link also to abstract and bio.


___

Prof. Stefano Baroni, Professor of theoretical condensed-matter physics 
at the Scuola Internazionale Superiore di Studi Avanzati (SISSA), 
Trieste, Italy


Gauge invariance of heat and charge transport coefficients
Tuesday, November 17, 2020, 15:00 (CET)
https://epfl.zoom.us/j/82989047900 with passcode 3214
https://nccr-marvel.ch/events/marvel-distinguished-lecture-stefano-baroni
___


I list below also the two following forthcoming lectures, by Silvia 
Picozzi and Jens Norskov.


Happy viewing,

nicola marzari





Prof. Silvia Picozzi, Director of Research at Consiglio Nazionale delle 
Ricerche (CNR) at the Institute for Superconducting and Innovative 
materials and Devices (SPIN) in Chieti, Italy


Spin-orbit coupling: a small interaction leading to rich physics
Tuesday, December 15, 2020, 15:00 (CET)
https://nccr-marvel.ch/events/marvel-distinguished-lecture-silvia-picozzi
_

Prof. Jens K. Nørskov, Professor of physics at the Technical University 
of Denmark (DTU)


Catalysis for sustainable production of fuels and chemicals
Tuesday, January 26, 2021, 15:00 (CET)
https://nccr-marvel.ch/events/marvel-distinguished-lecture-jens-norskov
_


--
--
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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] data/workflows positions at epfl

[Nicola Marzari]

Dear all,

in case it can be of interest, we have 2 positions at EPFL on data 
analytics, data integration, and simulation/machine-learning workflows - 
QE experience would be particularly precious. All info on applications 
(deadline Nov 6) at the link below.


nicola


https://psi-k.net/jobs/two-4-year-postdoctoral-positions-marzariepfl-o/


--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] Query regarding k path selection, mismatching of band gap

[Nicola Marzari]

On 13/10/2020 20:43, Poonam Kaushik wrote:

Dear Expert,
So the only option that I have is to include the complete path and do 
the calculation again.

Thank you so much for your suggestion.



Mostly welcome, but you have three options - destiny can be generous 
sometimes.


The first option would be doing a more careful DOS: 
https://www.quantum-espresso.org/Doc/INPUT_DOS.html


nicola




Thanks and regards,
Poonam Sharma




-
Poonam Sharma
Research Scholar
Department of Physics
Indian Institute of Technology Bombay
Mumbai - 400076
India.



On Tue, Oct 13, 2020 at 11:53 PM Nicola Marzari <mailto:nicola.marz...@epfl.ch>> wrote:





  From the most to the less likely, it could be that your DOS has some
broadening that masks the existence of a small gap, or that the gap
closes across the last two segments of the path that you are
missing, or
that you are very unlucky and the band gaps closes at points that do
not
lie on a high symmetry path.

              nicola


On 13/10/2020 19:53, Poonam Kaushik wrote:
 >
 > Dear Experts,
 >   I have one query regarding k path selection. After using Kpath
finder
 > (https://www.materialscloud.org/work/tools/seekpath ), i got 
this type

 > of  k path
 > G-M-K-G-A-L-H-A|L-M|H-K for my structure. In the calculation, I
used, up
 > to G-M-K-G-A-L-H-A. So, is this ok to select a path up to this?
 > Basically in the band structure, I am getting some finite gap
while in
 > dos I m getting a zero bandgap, after selecting the path up to
 > G-M-K-G-A-L-H-A. I am not able to figure out why this is happening?
 > Should it help to include the complete path? I am attaching here my
 > input file, band structure, and dos. Please have a look.
 >
 >
https://drive.google.com/drive/folders/1UhUgod8KnvdovJfxMqbJMQwdtb3dE-yY
 >
 >   I'll be very thankful for any suggestions.
 >
 > Thanks and regards,
 > Poonam Sharma
 >
 >
 >
 >

-
 > Poonam Sharma
 > Research Scholar
 > Department of Physics
 > Indian Institute of Technology Bombay
 > Mumbai - 400076
 > India.
 >
 >
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<mailto:users@lists.quantum-espresso.org>
 > https://lists.quantum-espresso.org/mailman/listinfo/users
 >


-- 
--

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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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--
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Re: [QE-users] Query regarding k path selection, mismatching of band gap

[Nicola Marzari]

From the most to the less likely, it could be that your DOS has some 
broadening that masks the existence of a small gap, or that the gap 
closes across the last two segments of the path that you are missing, or 
that you are very unlucky and the band gaps closes at points that do not 
lie on a high symmetry path.


nicola


On 13/10/2020 19:53, Poonam Kaushik wrote:


Dear Experts,
  I have one query regarding k path selection. After using Kpath finder 
(https://www.materialscloud.org/work/tools/seekpath ), i got  this type 
of  k path
G-M-K-G-A-L-H-A|L-M|H-K for my structure. In the calculation, I used, up 
to G-M-K-G-A-L-H-A. So, is this ok to select a path up to this?
Basically in the band structure, I am getting some finite gap while in 
dos I m getting a zero bandgap, after selecting the path up to 
G-M-K-G-A-L-H-A. I am not able to figure out why this is happening? 
Should it help to include the complete path? I am attaching here my 
input file, band structure, and dos. Please have a look.


https://drive.google.com/drive/folders/1UhUgod8KnvdovJfxMqbJMQwdtb3dE-yY

  I'll be very thankful for any suggestions.

Thanks and regards,
Poonam Sharma



-
Poonam Sharma
Research Scholar
Department of Physics
Indian Institute of Technology Bombay
Mumbai - 400076
India.


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--
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Director, National Centre for Competence in Research NCCR MARVEL, EPFL
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Re: [QE-users] Problems with Fe ONCV pseudopotential

[Nicola Marzari]

Related to this, we found a number of ghosts in the SG15, liaised with 
Francois, and that led to a number of updates in SG15.1 . Those are 
clearly visible in the band structure plots and matrix errors on the 
SSSP page.


E.g. compare SG15 and SG15.1:

https://www.materialscloud.org/discover/sssp/plot/precision/S

nicola



On 01/10/2020 10:48, Christoph Wolf wrote:
There is a "known problem" (known at least to Don Hamann, the creator of 
the ONCV), I will paste part of a conversation I had with him a few 
years ago pertaining to the same problem:


" The Fe SG15 input data must have been on the "hairy edge" of 
ghost behavior.  A small change of the local potential in the input 
should make it go away with the corrected 3.3.1, although I have not 
tested this yet.  It is unfortunate that some other SG15 input may have 
the same issue, and I'm confident that such a small local-potential 
change should not effect the quality of the psp, but the whole set 
apparently needs review.  Deep ghost detection was an innovation with 
3.3.0, although the SG15 automated input data refinement using real 
solid-state calculations would certainly have rejected data that 
produced ghosts  with 2.2.1 "


HTH!
Chris

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Re: [QE-users] Problems with Fe ONCV pseudopotential

[Nicola Marzari]

Dear MV,


you can find the tests for the SG15 pseudos on the SSSP pseudopotentials 
page - I checked the Fe, and it doesn't have any ghosts, at least in the 
elemental bulk form.


nicola



On 29/09/2020 12:59, mkondrin wrote:

On 29.09.2020 14:15, Lorenzo Paulatto wrote:
Thank you for your exhaustive and enlightening comment. I would 
rather stick to the abinit version of ONCV pseudopotentials. I really 
don't know which version I am using (at least I haven't managed to 
find the version number in the ONCVPSP folders). The zip-archive was 
downloaded 4 December 2019 and I believe it was the latest version at 
the moment.


Hello,
the version number is in the file name, it can be
 1.0 - January 2015
 1.1 - May 2015, not for all elements
 1.2 - (and not 1.5, as I incorrectly recalled) from June 2016, but only
    published ready-made in UPF version in February 2020

For Iron you have
Fe_ONCV_PBE-1.0.UPF
Fe_ONCV_PBE-1.2.UPF

I would say, try the 1.2 if the 1.0 has ghosts.
Many thanks again, Lorenzo. I believe I have downloaded ONCV 
pseudopotentials from the link in the official QE site 
(https://github.com/pipidog/ONCVPSP). It might be outdated, at least 
psedopotential files in it have no version number. The latest version of 
SG15 pseudopotentials can be downloaded from the original site 
http://www.quantum-simulation.org/potentials/sg15_oncv/ .


  Surely I give them a try.

Sincerely yours,
M.V. Kondrin


cheers




Sincerely yours,
M.V. Kondrin
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Re: [QE-users] About the Fermi level determination algorithm in q-e.

[Nicola Marzari]

On 15/09/2020 09:47, Hongyi Zhao wrote:

Hi,

I try to figure out the Fermi level determination algorithm in q-e but
still not so clear on the procedure implemented currently.

Any hints for this question?



bisection method

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Re: [QE-users] How to determine degauss

[Nicola Marzari]

My suggestion is that 0.02 Ry of either mp or mv is a very good choice - 
with this smearing, make sure things are converged with respect to 
k-points. If the quantity you are after is very sensitive to details of 
the fermi energy, going to 0.015 or 0.01 Ry, but never below, is a 
possibility - but typically you'll need many more k-points.


Here you can find a detailed explanation:
http://theossrv1.epfl.ch/Main/ElectronicTemperature

nicola


On 20/08/2020 03:56, Nitol, Mash wrote:

You can do a convergence study with energy same as estimating K points grid

Get Outlook for iOS <https://aka.ms/o0ukef>

*From:* users  on behalf of 
John McFarland 

*Sent:* Wednesday, August 19, 2020 8:54:18 PM
*To:* users@lists.quantum-espresso.org 
*Subject:* [QE-users] How to determine degauss
Hi, is there a recommended degauss? or procedure for determining a good 
estimate?


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Re: [QE-users] Phonon Density of States by atomic type

[Nicola Marzari]

On 03/08/2020 18:39, Baer, Bradly wrote:

Hello,

I was consulting the reference materials on materialsproject.org 
<https://materialsproject.org/materials/mp-830/> for a semiconductor.  
In the section on phonon results, they had the phonon density of states 
plotted with the contributions of each type of atom as well as the total 
DOS.    I have calculated the DOS of a system before using QE, but only 
did the total DOS of the system.  Does QE have the capability to give 
similar results?


Thanks,
Brad



Dear Brad,


for phonons I do not think there is any ready-made tool (but I could be 
wrong). For phonon dispersions, we have implemented an online phonon 
visulizer, based on the code by Henrique Miranda:

https://www.materialscloud.org/work/tools/interactivephonon
that allows you to explore graphically/interactively phonon dispersions
https://www.materialscloud.org/discover/2dstructures/details/BN

For the phonon DOS, if you have done a calculation with QE, you can at 
zero cost interpolate/diagonalize the dynamical matrices on fine q 
meshes, and build the DOS yourself. But maybe others have some tool 
ready to use.


nicola





Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University



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Re: [QE-users] [QE-developers] Problem regarding installation

[Nicola Marzari]

Thanks Pietro! Subir,

you can also download a virtual machine with QE already compiled and 
ready to run at https://www.materialscloud.org/work/quantum-mobile


nicola

On 26/07/2020 14:27, Pietro Delugas wrote:

Dear Subir

mails about subject like there are more suited to the users mailing list 
us...@quantum-espresso.org.


you may find installation instructions here: 
http://www.quantum-espresso.org/Doc/user_guide.pdf


best wishes

Pietro

On 26/07/20 11:34, Subir Ghosh wrote:
Sir i'm a Mtech student in Electronics Domain,i need this software for 
my final year project purpose regarding simulations of 2D materials.
tried to install the software several times but could not complete the 
installation properly, sir kindly provide me a proper installation 
guide which can help with the installation.

*_My System Configuration is_*
Processor - Core i5(3rd gen)
Ram - 4 GB
Hard Disc - 500 GB
OS - Windows 10

Kind & Regards
Subir Kumar Ghosh
(Jadavpur University)

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Re: [QE-users] Wrong position of fermi level in bulk Cr2O3

[Nicola Marzari]

    9.3433763434
O             0.7222569078        1.2509852624        9.3433763434
O            -0.7222575680        3.9164369549       11.4196834856
O            -0.7222547296        1.4144694992       11.4196834856

I later tried with pw91 USPP, it fixed the fermi level position (it's 
now at HUMO edge) but the bad gap is now very underestimated to 2.3 eV.


I tried paw but it wasn't working with me.

Can someone please help?

Regards

Yuvam Bhateja

IIEST Shibpur

India


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Re: [QE-users] Different kinds of pseudopotentials used in one calculation

[Nicola Marzari]

On 22/07/2020 12:40, Leo Yang wrote:

Dear QE users,

I have a question: Is that forbidden to use two different type of 
pseudopotentials in one calculation (e.g. Use norm-conserving 
pseudopotential for C, ultrasoft pseudopotential for O)? Could it 
produce any error? It will be very appreciated if you can solve my silly 
problem. Thanks.


Best,


it's ok to do so.


Yang Zhou
University of Leeds

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Re: [QE-users] oscillating energy value during optimization

[Nicola Marzari]

2976  -1.443293  14.413944
W       5.288433  -1.443790  14.404037
N       3.219452   5.199606  12.448287
N       7.366466   5.188650  12.437657
N       3.207970   0.704887  12.465361
N       7.371281   0.697722  12.461527
W       3.205392   3.068813  12.535650
W       7.371059   3.075963  12.535225
W       3.208342  -1.417371  12.526978
W       7.371423  -1.415702  12.526259
N       1.126718   3.566876  12.355498
N       5.287387   3.570864  12.349260
N       1.127573  -0.926625  12.347835
N       5.290289  -0.925589  12.354591
W       1.124934   5.676097  12.168934
W       5.300233   5.687505  12.124192
W       1.125212   1.183514  12.166731
W       5.291832   1.185520  12.166744
N       3.207882   3.506729  10.422372  0 0 0
N       7.371462   3.506729  10.422372  0 0 0
N       3.207882  -0.986715  10.422372  0 0 0
N       7.371462  -0.986715  10.422372  0 0 0
W       3.207882   5.716584  10.333236  0 0 0
W       7.371462   5.716584  10.333236  0 0 0
W       3.207882   1.223140  10.333236  0 0 0
W       7.371462   1.223140  10.333236  0 0 0
N       1.126093   6.199382  10.052766  0 0 0
N       5.289672   6.199382  10.052766  0 0 0
N       1.126093   1.705938  10.052766  0 0 0
N       5.289672   1.705938  10.052766  0 0 0
W       1.126093   3.871912  10.00  0 0 0
W       5.289672   3.871912  10.00  0 0 0
W       1.126093  -0.621532  10.00  0 0 0
W       5.289672  -0.621532  10.00  0 0 0
C       4.904436   5.088998  16.341705
H       4.817236   4.340738  17.152672
H       4.810563   5.831388  17.155825
H       3.209512   2.314472  17.745318
H       3.207503   3.080782  17.746006


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Re: [QE-users] why scf calculation give : Error in routine cell_base_init (1): lattice parameter not specified

[Nicola Marzari]

     22.699544770   1.884507541  -0.017095152
O       24.317254213   0.948550495   4.559888347
O       22.696355527   1.882427413   1.962689308
Zn      22.696414368   3.753053312   2.580573148
Zn      21.079772245   4.690040067  -0.017095329
O       22.696505254   3.753106740   4.559898944
O       21.076376280   4.688319995   1.962689887


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Re: [QE-users] About the k-points weights used for nscf calculation of pwscf.

[Nicola Marzari]

On 30/06/2020 13:07, Hongyi Zhao wrote:

As you can see, it uses 0.0156250 as the weight of all k-points. I
can't figure out how to obtain this value.


How much did you try? You have 64 k-points, the weights are all equal, 
what could possibly be this value? Anyhow, here is the magic:


1/64=0.015625


It said that for a non-scf calculation, weights do not affect the
results. If so, why they still set weights for the k-points in the
example I mentioned above?


Because one could go into a mode, in the future, where the wannier code 
uses only the points in the irreducible wedge, or at the very least it 
uses time reversal.


nicola



Any hints will be highly appreciated.




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Re: [QE-users] Wrong Fermi level with smearing compared to tetrahedra

[Nicola Marzari]

Hi,

Fermi energy is not really defined in an insulator/semiconductor; at 0 
temperature any value in the gap a is good fermi energy, but better to 
talk about the chemical potential. At temperature is raised, it would be 
approximately start in the middle of the gap, and move away from that 
depending on how the conduction and valence DOS are. Maybe read the 
Ashcroft Mermin chapter on homogeneous semiconductors (27, I think).


A typical good choice for smearing (0.02 Ry, 0.15 A^-1 density of 
k-points) would give you the fermi energy in the middle of the gap, 
approximately, if you use gaussian smearing in an insulator. mv and mp 
should not be used for an insulator/semiconductor.


Also, mv has positive occupations, so something seems wrong with your 
plot - are you sure you are not using mp?


nicola

On 27/06/2020 14:56, 후신 부지드 wrote:

Dear QE users,


I tried to search a solution for this problem and looked to the previous 
posts but didn't work with me




I made scf calculation for bulk SnS2 with dft-d3 using occupations= 
'tetrahedra' I get the the fermi level Ef on top of the valence band as 
reported in the literature,


but when I try to use smearing the Ef will shifts about 1 eV to locate 
in the middle of the gap


I tried gaussian smearing and fd using a huge k points, but eventhough 
the energy converges to the value in tertahedra case, the Ef always 
shifts by ~ 1eV.


The only exception is mv smearing with 0.01 degauss it gives the right 
Ef, (but it has a tail with finite dos which is not seen in the gaussian 
case with wrong Ef, pls see the attached image) and when I try mv with 
0.005 degauss it also show wrong Ef even with huge k points.



Does anyone know why I'm getting this shift in Ef even though the energy 
is converged and the kpoint is large enough



Here is the input file for tetrahedra and smearing:



Tetrahedra:


&control
     calculation = 'scf'
     restart_mode='from_scratch'
     prefix = 'tet'
     outdir = '/home/outdir'
     pseudo_dir = '/home/pseudo'
     verbosity = 'high'
/

&system

     ibrav = 0,
     nat   = 6,
     ntyp  = 2,
     ecutwfc=80
     ecutrho=560
     vdw_corr = 'dft-d3'
     occupations='tetrahedra'
     nbnd=52
     lda_plus_u=.true.
     Hubbard_U(1)=9.0,
     Hubbard_U(2)=9.0,

/

&electrons
     conv_thr=1e-6
/

ATOMIC_SPECIES
  Sn    118.71000  Sn.pbe-dn-kjpaw_psl.1.0.0.UPF
  S  32.06600  S.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS (angstrom)

Sn  -0.01900   2.129228760   7.368473930
Sn   1.843967305   1.064612836   1.474204489
S    1.843967305   1.064612836   8.846101191
S   -0.01900   2.129228760   2.951831855
S   -0.0  -0.0  -0.005322640
S   -0.0   0.0   5.888946695

CELL_PARAMETERS (angstrom)

  3.687930810   0.0  -0.0
-1.843965405   3.193841769  -0.0
-0.0  -0.0  11.788538670
K_POINTS (automatic)
  20 20 6 0 0 0



Smearing



&control
     calculation = 'scf'
     restart_mode='from_scratch'
     prefix = 'smea'
     outdir = '/home/outdir'
     pseudo_dir = '/home/pseudo'
     verbosity = 'high'
/

&system

     ibrav = 0,
     nat   = 6,
     ntyp  = 2,
     ecutwfc=80
     ecutrho=560
     vdw_corr = 'dft-d3'
     occupations='smearing',smearing='gaussian',degauss=0.01
     lda_plus_u=.true.
     Hubbard_U(1)=9.0,
     Hubbard_U(2)=9.0,
/

&electrons
     conv_thr=1e-6
/

ATOMIC_SPECIES
  Sn    118.71000  Sn.pbe-dn-kjpaw_psl.1.0.0.UPF
  S  32.06600  S.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS (angstrom)

Sn  -0.01900   2.129228760   7.368473930
Sn   1.843967305   1.064612836   1.474204489
S    1.843967305   1.064612836   8.846101191
S   -0.01900   2.129228760   2.951831855
S   -0.0  -0.0  -0.005322640
S   -0.0   0.0   5.888946695

CELL_PARAMETERS (angstrom)

  3.687930810   0.0  -0.0
-1.843965405   3.193841769  -0.0
-0.0  -0.0  11.788538670
K_POINTS (automatic)
  32 32 10 0 0 0


Houcine BOUZID
Sungkyunkwan University,


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Re: [QE-users] SCF calculations on WN supercell not converging

[Nicola Marzari]

 0.400059  10.604083  10.00  0 0 0
W       4.563639  10.604083  10.00  0 0 0
W       8.727218  10.604083  10.00  0 0 0
C      10.809008   2.628097  19.75
H      10.177000   1.997000  20.383000
H      11.443000   1.997000  19.117000
H      10.177000   3.263000  19.117000
H      11.443000   3.263000  20.383000

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--
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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] CECAM Webinars - The importance of being H.P.C. Earnest

[Nicola Marzari]

Dear all,


in case you want to know the difference between QE and CERN - tomorrow 
(Thu, 3pm).


nicola



*CECAM Webinars - The importance of being H.P.C. Earnest*

Dear Friends and Colleagues,

The power of simulation and modeling is intimately related to the 
available computational resources, to the community’s awareness of these 
resources, and to its proficiency in their optimal exploitation. The 
relevance and impact of High Performance Computing (HPC) can be quite 
different depending on the specific area, but we are all confronted with 
the relationship between new methods and algorithms and their 
implementation in proficient codes. We are also increasingly solicited, 
by technological developments and political choices, to consider in our 
research aspects related to scalability, portability and optimal 
deployment of software on a rapidly evolving ecosystem of hardware 
architectures.


We invite you to join us in an exploration of the relevance of HPC as an 
enabler of leading-edge simulation and modeling in our new series of 
webinars


*The importance of being H.P.C. Earnest*

The focus of the series will be on the science made possible by 
combining state-of-the-art methods with optimal exploitation of 
supercomputing resources.


The first of the five webinars planned for this event will be held on 
*Thursday June 18 15:00-17:00 (CEST)* and broadcasted live on the CECAM 
YouTube Channel at: https://www.youtube.com/watch?v=-scLUoHmFo4


with the following program:

15:00   Welcome and Introduction, Ignacio Pagonabarraga (CECAM)

15:10   Nicola Marzari (EPFL): The great mysteries of computational 
science, and the marvelous opportunities


15:40   Claudia Filippi (University of Twente), Anthony Scemama 
(University of Toulouse III): Targeting Real chemical accuracy at the 
EXascale


16:10   Giulia Galli (University of Chicago & Argonne National 
Laboratory): The long and winding road: predicting and designing 
material and molecular properties through computation


16:40   Questions and Answers

If you have a YouTube or Google account, you will be able to ask 
questions during the talks using a chat. You can also send your 
questions via email to direc...@cecam.org 
<mailto:direc...@cecam.org><mailto:direc...@cecam.org>. A moderator will 
relay as many of these questions as possible to the speakers.


More information and up to date videos can be found at: 
https://www.cecam.org/cecam-webinars


Looking forward to your participation. Be well,

the CECAM team in Lausanne

PS: So far, we have been blessed with good fortune in our broadcasts. 
However, we are well aware of the dangers of tempting fate so a 
disclaimer is still in order. Should there be serious problems while we 
are live, we ask for your understanding. All seminars will be recorded 
and will be available long-term on the CECAM website.



--
------
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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] Strong dependance of DFT+U on projector choice

[Nicola Marzari]

Dear Julien,


Iurii or Matteo or others might comment, but indeed we are working to 
streamline some of these issues. A few comments:


1) DFT is not a theory of band gaps, and I do not really think DFT+U is 
either. I believe DFT+U (and other stuff, V, J, etc...) can do a great 
job in improving the energetics, but I'm not sure fitting the band gaps 
is a good idea.


2) I like orthoatomic more, because atomic, in principle, can apply the 
U twice, if two orbitals are not orthonormal (the part of the orbital(s) 
that is not orthonormal enters twice in the hubbard term)


3) the big difference that orthoatomic does is that it orthogonalizes 
every projector with every projector, so you become much more sensitive 
to the ligands


4) the linear response U accounts for different manifolds, and so it 
ameliorates the arbitrary dependence from the manifold. This was 
discussed in the appendix kulik-marzari jcp 2008.


5) in the long-term, I think we'll settle on orthoatomic, u, and v. it's 
a lot of work, done by Iurii Timrov and Matteo Cococcioni - most 
recently to add forces and stresses to the orthoatomic case.


nicola



On 17/06/2020 16:13, JULIEN, CLAUDE, PIERRE BARBAUD wrote:

Dear Users,
I have recently tried to implement DFT+U on a FAPbI3 system, following the work 
reported in J. Phys. Chem. C 2018, 122, 27340−27349. This is not the most 
canonical use of DFT+U on d orbitals of transition metals. Instead, the authors 
used the Hubbard correction on the I 5p and Pb 6p orbitals to empirically fit 
the experimental band gap.
Since this is used in conjonction with spin-orbit effects, I have to use 
lda_plus_u_kind=1 (but I keep J=0, which should make it equivalent to using the 
default method if I'm not mistaken). I also had to add the atoms in the 
relevant f90 files as they were not initially included.

When initially trying to correct the band gap, I observed very troubling results. The 
band gap actually reduced from ~0.4 eV (DFT w/SOC) to ~0.3 eV (DFT+U w/SOC). Even more 
frustrating, screening multiple U values made very little change on that band gap result, 
and would always yield values lower than the U=0 case... Another disturbing result had to 
do with the occupancy eigenvalues, which reported a total occupation of 3.4 on Pb, 
seemingly making it a "Pb-". This is strange because the bonding in this 
material has an ionic character, and I would expect Pb oxidation state  to tend towards a 
Pb2+ (meaning its occupation should at least go below 2). I tried to force different 
behaviors with lower values for starting_ns_eigenvalue, but unsuccessfully.

I then noted that the projectors I was using were not orthogonalized, which 
makes the interpretation in terms of ionic charges more challenging. I tried a 
run with U_projection_type='ortho-atomic', and this changed the results 
completely. I was able this time to obtain much larger band gaps and to find 
pairs of U value reproducing my experimental band gap easily. I do observe an 
occupation of 1.3 on Pb for those values, which seems more realistic too.

However, I am not very comfortable with this. Is it normal for my results to be 
so wildly influenced by the choice of projectors (it seems like a somewhat 
arbitrary choice that should not change completely the results obtained). The 
fact that I can't get anything to work with the default option (and especially 
that the band gap was reduced) is still quite disturbing, and makes me question 
the validity of the results obtained with orthonormal projectors.
Has this strong influence been reported before? Is it the symptom of a problem 
that can invalidate further calculations?
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----------
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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] Newly-engineered Materials Cloud Archive unveiled

[Nicola Marzari]

Thank you Giovanni! Let me try to repost below with hopefully firendlier 
formatting - apologies to all for the double posting!


nicola



Dear Quantum ESPRESSO users,

we would like to announce the launch of a newly engineered Materials 
Cloud Archive <https://archive.materialscloud.org/>, now powered by the 
same Invenio framework as the massive Zenodo 
<https://zenodo.org/>repository at CERN.


The Materials Cloud Archive <https://archive.materialscloud.org/>, 
active since March 2017, is a public, free, open-access repository for 
research data and tools in computational materials science and in 
related experimental efforts, inspired by the archive initiatives for 
preprints. It provides the capability to upload and persist arbitrary 
data records from anyone in the community with a minimum guaranteed 10 
year retention time per record. Currently, 0.5 petabytes are already 
allocated; the  limits for standard submissions are of 5 GB for data 
sets in any format, and of 50 GB for AiiDA databases; moderators can 
approve larger data sets upon request. Each entry is assigned a globally 
unique and persistent digital object identifier (DOI) and harvestable 
metadata. The new Invenio platform makes it easier for authors to submit 
and later update data records, provides full-text searches, and powers 
streamlined workflows for content moderation.


The Archive is an integral part of the Materials Cloud 
<https://www.materialscloud.org/>FAIR data infrastructure, in 
partnership with several European and national centres - these include 
the MaX <http://www.max-centre.eu/>Centre of Excellence, the MARVEL 
<https://nccr-marvel.ch/>NCCR, the H2020 MarketPlace 
<https://www.the-marketplace-project.eu/>, NFFA <http://www.nffa.eu/>, 
and Intersect <http://intersect-project.eu/>projects, EMMC 
<https://emmc.info/>, swissuniversities 
<https://www.materialscloud.org/swissuniversities>, PASC 
<https://www.pasc-ch.org/>,and OSSCAR <https://www.osscar.org/>. It is a 
recommended repository for Nature’s Scientific Data 
<https://www.nature.com/sdata/policies/repositories#materials>, it is 
indexed by FAIRsharing <https://fairsharing.org/biodbcore-001089/>, 
Google Dataset Search 
<https://datasetsearch.research.google.com/search?query=Materials%20Cloud>and 
EOSC-hub <https://www.eosc-hub.eu/>/EUDAT <https://www.eudat.eu/>’s 
service B2FIND <http://b2find.eudat.eu/group/materialscloud>, and it is 
registered on re3data <https://www.re3data.org/repository/r3d100012611>. 
Finally, it is an official implementation network 
<https://www.go-fair.org/implementation-networks/overview/materials-cloud/>of 
the GO FAIR initiative <https://www.go-fair.org/>.


More information on the Materials Cloud integration of data, workflows 
and codes can be found in L. Talirz et al., Materials Cloud, a platform 
for open computational science, arXiv:2003.12510 (2020) 
<https://arxiv.org/abs/2003.12510>and in S. Huber et al., AiiDA 1.0, a 
scalable computational infrastructure for automated reproducible 
workflows and data provenance, arXiv:2003.12476 (2020) 
<https://arxiv.org/abs/2003.12476>.


The new Materials Cloud Archive infrastructure has been unveiled today 
(Wednesday 27th May 2020), during the MaX webinar <http://www.max 
centre.eu/webinar/managing-simplifying-and-disseminating-high-throughput-computational-materials-science-aiida>(part 
of the ongoing MaX webinar series <http://www.max-centre.eu/webinar>on 
advances toward exascale computing) that focused on FAIR and 
reproducible high throughput computational science as enabled by AiiDA 
and AiiDA lab, Quantum ESPRESSO and SIRIUS, and the Materials Cloud 
Archive. Videos of the presentations will be available online from 
tomorrow (28th May) on the webpage of the event 
<http://www.max-centre.eu/webinar/managing-simplifying-and-disseminating-high-throughput-computational-materials-science-aiida>.


With warmest regards,

Giovanni Pizzi, Nicola Marzari, and the Materials Cloud team


--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] Huge memory requirements for a scf calculation of a system consisting with 300+ atoms.

[Nicola Marzari]

Fully agree with this! If I can add, using the Baldereschi point (or, to 
make it simple, 1/4 1/4/ 1/4 in crystal coordinates), and nosym=.true. 
allows you to do a calculation with one k-point that is almost as 
accurate as using a 2x2x2 shifted monkhorst pack mesh (i.e. 2 2 2 1 1 
1), at a cost that is only twice as large as a Gamma only calculation.


If a metal, use 0.03 Ry of smearing (either m-p or m-v), and indeed you 
are good to go for a fast but quite accurate relaxation.


nicola

On 27/05/2020 13:39, Giuseppe Mattioli wrote:


Dear all
Just to add a bit of personal experience that might be useful to others. 
Let's admit that many k-points are necessary to provide a good 
description of the electronic properties of a given system, this is 
generally true in the case of metal systems. This fact might not extend 
to the potential, and very tiny differences might be found in final 
structures optimized by using a coarser sampling of the Brillouin zone. 
In the huge cell shared by Hongyi Zhao, I would start a geometry 
optimization from a gamma-only simulation and then I would check if 
forces on ions were low enough with a 2x2x1 mesh. If this was not the 
case, I would fully optimize the system with the new mesh and go a step 
ahead, and so on up to a decent convergence of the potential. Then I 
would perform nscf calculations with increasing numbers of k points 
followed by, e.g., dos.x post processing runs, to check the convergence 
of the density of states (be careful, because AFAIK nscf runs overwrite 
the results of the scf run). Of course, all of this depends on the 
specific purpose of the calculation, but in my past experience with 
molecules on metal surfaces this strategy saves a lot of time and 
resources.

HTH
Giuseppe

Quoting Sebastian Hütter :


Hi,

This may be a stupid question, but...


 Estimated static dynamical RAM per process >   3.32 GB
 Estimated max dynamical RAM per process >  10.52 GB
 Estimated total dynamical RAM > 462.96 GB


... is this not expected behavior? I'm not super experienced, so I 
just assumed it was.


Your numbers pretty much match what I see in terms of "RAM per Cell 
volume" in metals with non-symmetric unit cells using PAW pseudos, if 
not less. Random example: 126 atoms, 63 k-points, ~1000 bands, 250³ 
dense grid FFT gives ~10GB per rank, for a total of 680GB with 64 
ranks. I actually plan node requests for our cluster based entirely on 
memory required, probably wasting CPU time along the way (4N*16C in 
the example above).


Reasonable ke and charge cutoffs seem to blow up the memory 
requirements a lot. Of course multiplied by the number of bands...



Best,

Sebastian


--
M.Sc. Sebastian Hütter
Otto-von-Guericke University Magdeburg
Institute of Materials and Joining Technology
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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: 

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--
----------
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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] Charged Convergence Issues

[Nicola Marzari]

Thanks Giuseppe!

Indeed, with Oliviero we studied this class of problems (unbound anions, 
and their absorption on metal slabs). The discussion is here:

https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00552 (also on arxiv).

In a nutshell, the "correct" bound state is there, but in vacuum the 
unbound state is lower in energy, so that's where DFT-PBE converges to.


In the presence of continuum solvation, the "correct" bound state 
becomes the lowest in energy, so that's where the calculation converges 
to. Since these energies are linear in the dielectric constant of the 
medium, you can extrapolate to the vacuum case.


I say "correct" because the anion would still have self-interaction 
errors - they seem to be smaller than I would have thought, meaning the 
the damaging effect of self-interaction is stabilizing the wrong state, 
but the correct "excited" state has good energies. Same reason why 
penalty functionals or constrained-DFT work well for charge-transfer 
excitation - they do not fix the errors of approximate DFT, but allow 
you to select your "ground" state that approximate DFT makes an excited 
state. Piece of cake...


nicola



On 19/05/2020 09:45, Giuseppe Mattioli wrote:


Dear Robert
The calculation does not converge due to delocalization error (see, 
e.g., Cohen et al., Science 2008, 321, 792), which affect local (LDA) 
and semilocal (GGA) functionals. The excess electron of COO- is unbound 
in your DFT description of the system and hinders scf convergence. On 
the other hand, COO- is not stable in gas phase, while it is stable in 
water solution. There are a few possible things to do:


1) use a hybrid GGA+EXX functional that partially corrects the 
delocalization error. It helps but COO- (gas) may still contain an 
unbound electron.
2) embed your system in an implicit solvent with the QE plugin (see 
quantumenviron.org for details)
3) use 2) together with the explicit inclusion of a first solvation 
sphere (e.g., a few explicit water molecules) which lower the energy of 
the unbound electron and stabilize COO-, favoring convergence.

HTH
Giuseppe

Quoting Robert Stanton :


Hello,

    I'm having an issue in calculating adsorption energies in a system 
with

charged molecules. I have relaxed the structure with and without the
adsorbent. In the case of structure+adsorbent, I introduce a compensating
jellium background charge for the COO- molecule, and this converges fine.
The structure itself is neutral and converges fine in a neutral cell.
However I need to also optimize the lone COO-, and I am running into the
issue that this will not converge in the case of a charged cell, but 
only a

neutral one. The issue then is that if I use the COO- energy converged in
the neutral cell, I get adsorption energies that are not accurate.

    I am mainly just wondering how the calculation is converging in the
latter two cases above, since from what I've read it seems one of them
should have a charged cell causing convergence issues? Could cutoffs
potentially be causing an issue here? I have tried adding spin
polarization, dropping the mixing beta extremely low, and tried other 
small

molecules with a formal charge and they all have a similar issue. Just
looking for any ideas as to how I could get this charged molecule to
converge alone in a charged cell.

Thank you in advance,
Robert Stanton
Clarkson University




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, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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Re: [QE-users] error message: wrong offset

[Nicola Marzari]

Ooops - you want SOC. Check carefully the cutoff, then - the non 
relativistic version needed 140 Ry.


nicola



On 12/05/2020 18:29, Nicola Marzari wrote:



Dear all,

I'm a bit tired of repeating this - but why would you want to use Eu 
from the PSLibrary?


https://www.materialscloud.org/discover/sssp/plot/efficiency/Eu


     nicola


On 12/05/2020 18:09, Timrov Iurii wrote:

Here are the posting guidelines:

https://www.quantum-espresso.org/forum


Which QE version do you use? What is your input file?


Iurii


--
Dr. Iurii Timrov
Postdoctoral Researcher
STI - IMX - THEOSand NCCR - MARVEL
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 
Adrian Popescu 

*Sent:* Tuesday, May 12, 2020 5:55:05 PM
*To:* users@lists.quantum-espresso.org
*Subject:* [QE-users] error message: wrong offset
Hello,

I am trying to run a scf calculation for europium with spin-orbit 
coupling and LDA+U and I get the following error:

from offset_atom_wfc: error #
wrong offset
I see from the archived posts that this may be caused by the 
pseudopotential not containing the wave functions information. 
However, the pseudopotential I am using (from the Quantum Espresso web 
page PSLibrary) contains this information and has_wfc = .true.

Any ideas on how to get over this issue?
Thank you,

Adrian Popescu
Postdoctoral researcher
University of South Florida

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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] error message: wrong offset

[Nicola Marzari]

Dear all,

I'm a bit tired of repeating this - but why would you want to use Eu 
from the PSLibrary?


https://www.materialscloud.org/discover/sssp/plot/efficiency/Eu


nicola


On 12/05/2020 18:09, Timrov Iurii wrote:

Here are the posting guidelines:

https://www.quantum-espresso.org/forum


Which QE version do you use? What is your input file?


Iurii


--
Dr. Iurii Timrov
Postdoctoral Researcher
STI - IMX - THEOSand NCCR - MARVEL
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 
Adrian Popescu 

*Sent:* Tuesday, May 12, 2020 5:55:05 PM
*To:* users@lists.quantum-espresso.org
*Subject:* [QE-users] error message: wrong offset
Hello,

I am trying to run a scf calculation for europium with spin-orbit 
coupling and LDA+U and I get the following error:

from offset_atom_wfc: error #
wrong offset
I see from the archived posts that this may be caused by the 
pseudopotential not containing the wave functions information. However, 
the pseudopotential I am using (from the Quantum Espresso web page 
PSLibrary) contains this information and has_wfc = .true.

Any ideas on how to get over this issue?
Thank you,

Adrian Popescu
Postdoctoral researcher
University of South Florida

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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] Different implementations of the Hubbard 'U' between QE and VASP

[Nicola Marzari]

On 06/05/2020 22:02, Shivesh Sivakumar wrote:

Nicola,

Sorry to bring up the subject again but I still can't reconcile 
something. I understand that 'U' is not universal and not completely 
portable between different PPs. But what I find odd is the effect of 
'U'. On QE (with NCPP), 'U' seems to suppress the band gap whereas in 
VASP (with PAW), 'U' seems to widen the band gap. This is what looked 
very strange.


Best,
Shivesh


Not sure what to say - i.e. one would really need to delve deep into the 
case study. I think the VASP PAW projectors that are used for the U are 
strictly localized inside the core, and so might be quite a bit 
different from those of say a NCPP pseudo. But this is the kind of 
question that can be answered only by a detailed study - do you get with 
no U the same results?


Where did you get the Cr norm-conserving pseudo? Is it any good?
Our recommendation is the USSP from the GBRV work of David Vanderbilt:
https://www.materialscloud.org/discover/sssp/plot/precision/Cr

nicola


----------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
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Re: [QE-users] Different implementations of the Hubbard 'U' between QE and VASP

[Nicola Marzari]

Dear Shivesh,


this is really important: as Iurii and Paolo already mentioned, U is 
*not* a universal parameter. For the same element and for the same 
material, it can be easily 3eV or 7eV (e.g. if the Hubbard manifold it 
acts upon has been taken say from a pseudopotential (NCPP/USPP/PAW) 
generated in a neutral configuration or in an oxidized one).


So, that means that the same identical material - say, MnO - should be 
studied using a U for Mn of 3.13 if you use pseudopotential "A", and 
7.56eV when you use pseudopotential "B" for Mn. For a slightly 
compressed unit cell, maybe the U for "A" would be 3.10eV, and for "B" 
7.74eV.


Looking at the literature wouldn't help - especially (IMNSHO) because 
almost noone has understood what the U is.


nicola



On 06/05/2020 18:25, Shivesh Sivakumar wrote:

Timrov and Paolo,

Thank you very much for your wonderful inputs. I just wanted to clarify 
a few things that I might have left out in my original message.
When I said I used the same parameters for both calculations, this is 
what I meant:
a) Relaxed it in QE ( and then moved to scf etc..). For VASP, I used the 
relaxed structure to directly perform scf calculation, therefore the 
structure shouldn't cause any problems between the two.
b) Used a well tested (for convergence) k point grid on QE. Used the 
same k mesh for VASP.
c) The same smearing parameters and same hubbard U value ( of 3 eV - for 
the Chromium atom in my system) for both calculations.


Regarding your final question, yes, I did not compute 'U' from 
first-principles. It was assumed after referring to various 
literature about the same material.


Best,
Shivesh

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------
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Re: [QE-users] High symmetry path and k points

[Nicola Marzari]

On 22/04/2020 13:10, Lorenzo Paulatto wrote:
1). In any high symmetry, path let say Silicon Γ—X—U|K—Γ—L—W—X, what 
is the meaning of U|K,


Hello, there is no standard for giving list of k-path points, you should 
ask to who gave you the string to be sure. My guess is that you have two 
paths: Γ—X—U and K—Γ—L—W—X



Hi all,


for ref - an effort to standardize k-point paths according to 
crystallographic conventions has been made by Yoyo Hinuma and Giovanni 
Pizzi and Isao Tanaka - you can find the paper at the link below, and 
also a tool for Quantum ESPRESSO that gives you automatically the 
standard k-point path. This is for 3D systems.


nicola


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

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Re: [QE-users] Seeking help for SCF calculations on possible semiconductor (Based on several error reports)

[Nicola Marzari]

On 15/04/2020 11:18, zhangk...@mail.sysu.edu.cn wrote:

Dear experts,

I am currently doing an scf calculation and have encountered several 
blocks here. Here is the input script:




Try the QE input generator,

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

choose the option "magnetic".

nicola




&system
     ibrav   =   4
     celldm(1)   =  15.227846653
celldm(2)   =  1
celldm(3)   =  0.4640435926996375
celldm(4)   =  120.000
celldm(5)   =  90.000
celldm(6)   =  90.000
     nat =   3
     ntyp    =   2
ecutwfc = 33.07
nspin = 2
tot_magnetization=0.4285714
/
  &electrons
     conv_thr    =   1.D-12
     diagonalization =  'cg'
/
ATOMIC_SPECIES
C  12.01  C_ONCV_PBE_fr.upf
N  14.01  N_ONCV_PBE_fr.upf
ATOMIC_POSITIONS {crystal}
C  0.    0.    0.9974228266286470
C  0.    0.    0.3359239109776594
N  0.    0.    0.531993936927
K_POINTS {automatic}
10 10 18 0 0 0


Firstly I was blocked by forgetting the system is spin-polarized and 
adding nspin=2; And then got stuck here:fixed occupations and lsda need 
tot_magnetization, *here the point: I have difficulties on how to 
specify the magnetization related variables. Why these variables must be 
specified? *I got the first error in warning to add smearing, but it 
supposed that this system should be a semiconductor. And then, based on 
the first point, I have tried to execute a vasp calculation and extract 
the magnetization=0.4285714 from OUTCAR (I am not sure if this set is 
suitable). The after error report is: Error in routine card_kpoints 
(1):error while reading automatic k points.


I am afraid that this will be a dead cycle. So I am here to seeking some 
suggestions, sincerely.


Kan Zhang

from Sun Yat-sen University,China






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Re: [QE-users] 3drism-enabled qe

[Nicola Marzari]

On 08/04/2020 15:28, Shaofeng Wang wrote:

3drism-enabled qe



Google points to this:
https://www.quantum-espresso.org/download
(not sure if it's 3D-RISM or 1D-RISM).

For solvation and electrolytes, Oliviero Andreussi and some of us 
develop also quite actively http://www.quantum-environ.org


nicola

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Re: [QE-users] Fireside chats for lockdown times: A gentle introduction to density-functional theory

[Nicola Marzari]

Ooops - apologies for the reply to all.

nicola

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Re: [QE-users] Fireside chats for lockdown times: A gentle introduction to density-functional theory

[Nicola Marzari]

Dear Ian,


very nice to hear from you! Carey here in cc was going to prepare a 
tweet for our MARVEL NCCR - you'd be superwelcome to retweet or do one 
of your own - whatever you prefer. And thanks a lot!


We do not do facebook, so again mostly welcome there!

nicola



On 07/04/2020 22:35, Ian Shuttleworth wrote:

Nicola,

I think this is a great idea. Is the following link 'share-able' to 
social media?


https://www.materialscloud.org/learn/sections/spVa3j/fireside-chats-for-lockdown-times

When I try to invite taught students to this type of event, I use a 
combination of Facebook / Twitter because - I'm assured - students read 
that sort of thing. Occasionally, promotion this way seems to work, so 
would it be possible in this case?


With thanks

Ian Shuttleworth
(Nottingham Trent University)



On Tue, Apr 7, 2020 at 7:02 PM Nicola Marzari <mailto:nicola.marz...@epfl.ch>> wrote:




Dear friends,


a number of colleagues have asked me where to find more information on
quantum-mechanical simulations during these lockdown times - since I've
been teaching density-functional theory for a while, I've decided to
organize 3 public live webinars on the topic, each 2 hours long
(including a break). These are aimed either at experimental colleagues
that want to learn more about the field, or at researchers that want to
start learning more about simulations - feel free to distribute to
those
you think might be interested.


Wed Apr 15, 3pm-5pm CEST: *Density-functional theory.* An introduction
to electronic-structure methods and in particular density-functional
theory. Suitable for everyone that wants to learn what DFT is.

Thu Apr 16, 3pm-5pm CEST: *Density-functional practice.* An
introduction
to calculations using the total energy, planewaves, pseudopotential
method. Suitable for everyone that wants to learn how to perform a DFT
calculation. A self-learning handout and a virtual machine with
pre-installed open-source quantum-simulation codes are also available -
we'll use Quantum ESPRESSO.

Fri Apr 17, 3pm-5pm CEST: *Applications and limitations.* An
introduction to the properties that can be calculated with DFT, their
accuracy, and the practical or conceptual limitations for such
calculations. Suitable for everyone that wants to learn what can, or
cannot, be done with DFT. Will also answer the perennial question "Why
is DFT like Tinder?".


Details on how to follow these 3 webinars are given below - note that
you'll need a 4-digit password (the year in which Walter Kohn won the
Nobel prize). The webinar videos will be recorded and made available
(together with the slides) in the Learn section of the Materials Cloud
(https://www.materialscloud.org/learn); during the webinar,
participants
will be able to type questions in the live chat; answers to the most
topical ones will be provided later in a PDF file, also in the Learn
section. For those wanting to try their hands at simulations, there
will
be the chance to do so after the second webinar, using the Quantum
Mobile virtual machine, that can run on any computer (Windows, Max,
Linux...) with an Ubuntu Linux environment pre-installed with many
open-source simulation codes (we'll use Quantum ESPRESSO). Links to the
Quantum Mobile and the GitHub tutorial material (this latter to be
finalized in the next few days) will also be available in the Learn
subsection. All information below - with many thanks to MARVEL and MaX,
for the IT infrastructure (https://nccr-marvel.ch/ and
http://www.max-centre.eu/)), and to all the team and partners of the
Materials Cloud (https://www.materialscloud.org/team,
https://www.materialscloud.org/home#partners).

I'll conclude with our call for more virtual education and conferences:
Less carbon, more silicon!

                          nicola marzari


Main website: https://www.materialscloud.org/learn - go to the section
"Fireside chats for lockdown times", subsection "A gentle introduction
do DFT calculations - April 2020"

Webinars: details on the http links and password are below. These will
be given on Apr 15/16/17 2020, at 3pm CEST (that's Central European
Summer Time - i.e. the current time in Rome/Berlin/Paris - you can find
your local time at https://time.is/compare/1500_15_Apr_2020_in_CEST).

Note that there is a maximum limit of 500 participants, and things can
go wrong, so if anything does, videos and all material will in any case
be posted in the Materials Cloud Learn section
(https://www.materialscloud.org/learn), together with all relevant info
for those interested.

Password: a 4-digit number - the year in which W

[QE-users] Fireside chats for lockdown times: A gentle introduction to density-functional theory

[Nicola Marzari]

Dear friends,


a number of colleagues have asked me where to find more information on 
quantum-mechanical simulations during these lockdown times - since I've 
been teaching density-functional theory for a while, I've decided to 
organize 3 public live webinars on the topic, each 2 hours long 
(including a break). These are aimed either at experimental colleagues 
that want to learn more about the field, or at researchers that want to 
start learning more about simulations - feel free to distribute to those 
you think might be interested.



Wed Apr 15, 3pm-5pm CEST: *Density-functional theory.* An introduction 
to electronic-structure methods and in particular density-functional 
theory. Suitable for everyone that wants to learn what DFT is.


Thu Apr 16, 3pm-5pm CEST: *Density-functional practice.* An introduction 
to calculations using the total energy, planewaves, pseudopotential 
method. Suitable for everyone that wants to learn how to perform a DFT 
calculation. A self-learning handout and a virtual machine with 
pre-installed open-source quantum-simulation codes are also available - 
we'll use Quantum ESPRESSO.


Fri Apr 17, 3pm-5pm CEST: *Applications and limitations.* An 
introduction to the properties that can be calculated with DFT, their 
accuracy, and the practical or conceptual limitations for such 
calculations. Suitable for everyone that wants to learn what can, or 
cannot, be done with DFT. Will also answer the perennial question "Why 
is DFT like Tinder?".



Details on how to follow these 3 webinars are given below - note that 
you'll need a 4-digit password (the year in which Walter Kohn won the 
Nobel prize). The webinar videos will be recorded and made available 
(together with the slides) in the Learn section of the Materials Cloud 
(https://www.materialscloud.org/learn); during the webinar, participants 
will be able to type questions in the live chat; answers to the most 
topical ones will be provided later in a PDF file, also in the Learn 
section. For those wanting to try their hands at simulations, there will 
be the chance to do so after the second webinar, using the Quantum 
Mobile virtual machine, that can run on any computer (Windows, Max, 
Linux...) with an Ubuntu Linux environment pre-installed with many 
open-source simulation codes (we'll use Quantum ESPRESSO). Links to the 
Quantum Mobile and the GitHub tutorial material (this latter to be 
finalized in the next few days) will also be available in the Learn 
subsection. All information below - with many thanks to MARVEL and MaX, 
for the IT infrastructure (https://nccr-marvel.ch/ and 
http://www.max-centre.eu/)), and to all the team and partners of the 
Materials Cloud (https://www.materialscloud.org/team, 
https://www.materialscloud.org/home#partners).


I'll conclude with our call for more virtual education and conferences: 
Less carbon, more silicon!


nicola marzari


Main website: https://www.materialscloud.org/learn - go to the section 
"Fireside chats for lockdown times", subsection "A gentle introduction 
do DFT calculations - April 2020"


Webinars: details on the http links and password are below. These will 
be given on Apr 15/16/17 2020, at 3pm CEST (that's Central European 
Summer Time - i.e. the current time in Rome/Berlin/Paris - you can find 
your local time at https://time.is/compare/1500_15_Apr_2020_in_CEST).


Note that there is a maximum limit of 500 participants, and things can 
go wrong, so if anything does, videos and all material will in any case 
be posted in the Materials Cloud Learn section 
(https://www.materialscloud.org/learn), together with all relevant info 
for those interested.


Password: a 4-digit number - the year in which Walter Kohn won the Nobel 
Prize.


Density-functional theory
Wed Apr 15, 3pm-5pm CEST
https://epfl.zoom.us/j/360496579?pwd=VlNtMCtjTW9oRndEalVsaEU0RVFNUT09
Password: a 4-digit number - the year in which Walter Kohn won the Nobel 
Prize.


Density-functional practice
Thu Apr 16, 3pm-5pm CEST
https://epfl.zoom.us/j/387981888?pwd=QThRMnExeXk1NXNqb0lPUlEwT0t3QT09
Password: a 4-digit number - the year in which Walter Kohn won the Nobel 
Prize.


Applications and limitations
Fri Apr 17, 3pm-5pm CEST
https://epfl.zoom.us/j/535473835?pwd=QjF2WTV4c3ZUbGZTT0RYOGJnKzE3Zz09
Password: a 4-digit number - the year in which Walter Kohn won the Nobel 
Prize.


Or an H.323/SIP room system:

H.323:
162.255.37.11 (US West)
162.255.36.11 (US East)
221.122.88.195 (China)
115.114.131.7 (India Mumbai)
115.114.115.7 (India Hyderabad)
213.19.144.110 (EMEA)
103.122.166.55 (Australia)
209.9.211.110 (Hong Kong)
64.211.144.160 (Brazil)
69.174.57.160 (Canada)
207.226.132.110 (Japan)

First webinar: (password as above)
Meeting ID: 360 496 579
SIP: 360496...@zoomcrc.com

Second webinar: (password as above)
Meeting ID: 387 98

Re: [QE-users] epsilon.x

[Nicola Marzari]

On 07/04/2020 17:57, Fariba Islam wrote:
I am using the pp Si.pbe-n-kjpaw_psl.1.0.0.UPF whose pp type is PAW 
still I am receiving the previous error-

task #         0
      from grid_build : error #         1
      USPP are not implemented



PAW is as complex as USPP, so the error message above comprises both cases.


And another question is where can I get norm-conserving pp?


We have tested the Schlipf Gygi, that you can find here:
http://www.quantum-simulation.org/potentials/sg15_oncv/

The tests are in
https://www.materialscloud.org/discover/sssp/plot/efficiency/Si


nicola




On Tue, Apr 7, 2020 at 9:45 PM Fariba Islam <mailto:ezq...@gmail.com>> wrote:


   I am sorry I misunderstood the error, I thought it said I need to
use USPP. But it said otherwise.
Thanks for your help.

On Tue, Apr 7, 2020 at 9:38 PM Nicola Marzari
mailto:nicola.marz...@epfl.ch>> wrote:

On 07/04/2020 17:32, Fariba Islam wrote:
 > I have used USPP Si.rel-pbe-nl-rrkjus_psl.1.0.0.UPF
 >

<https://www.quantum-espresso.org/upf_files/Si.rel-pbe-nl-rrkjus_psl.1.0.0.UPF> 
to

 > run scf and nscf for silicon. But when I run the epsilon.x
the program
 > crashes with the following error-
 > task #         0
 >       from grid_build : error #         1
 >       USPP are not implemented

What is the problem, in your opinion?

                         nicola


----------
Prof Nicola Marzari, Chair of Theory and Simulation of
Materials, EPFL
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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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] epsilon.x

[Nicola Marzari]

On 07/04/2020 17:32, Fariba Islam wrote:
I have used USPP Si.rel-pbe-nl-rrkjus_psl.1.0.0.UPF 
<https://www.quantum-espresso.org/upf_files/Si.rel-pbe-nl-rrkjus_psl.1.0.0.UPF> to 
run scf and nscf for silicon. But when I run the epsilon.x the program 
crashes with the following error-

task #         0
      from grid_build : error #         1
      USPP are not implemented


What is the problem, in your opinion?

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] [QE users] pseudopotential hardness and transferability

[Nicola Marzari]

Ciao Aldo,


a meaningful/useful test would be this - take a simple case of a CN
system - it can be as simple as an infinite 2-atom primitive cell of a 
graphene-like sheet (or a 2-atom primitive FCC cell (like GaAs)). 
Doesn't matter if it's not that physical. You also do not need fine 
k-point sampling. Shake one of the 2 atoms quite a bit - 10-15% of their 
typical bond lengths.


For this system, plot the total force on 1 atom, and the trace of the 
stress tensor, as a function of cutoff on the wavefunctions (30, 40, 50, 
60, 70, 80, 100 Ry) for a couple of duals (i.e. ecutrho six or 8 times 
larges than ecutwfc). If you feel good about doing it, look also at the 
frequencies of a phonon - maybe not Gamma, but at a zone boundary.


This will tell you what cutoffs you need for a structural relaxation.

Let me also repeat that the convergence on the total energy is not a 
necessary condition - you can have wonderful and accurate pseudos whose 
total energy is still changing at a cutoff that is good for forces and 
stresses.


nicola


On 03/04/2020 10:43, Aldo Ugolotti wrote:

Dear Nicola,

I share with you the perplexity about the unusual values for the 
cutoffs, that's why I wished to understand the origin of it and whether 
it could be improved or fixed (other than just setting such cutoff and 
keep going). About checking the pseudo versus the total energy, it might 
be not so relevant but indeed it is a necessary condition.


In my tests I just run scf calculations with different cutoffs/k-mesh 
with fixed geometry and extract the total energy (i.e. fixing the 
precision rather than the accuracy, in the language of Science, 351, 
2016, paper). I consider the minimal cutoff the one at which the total 
energy is within ~ 1mRy from the value of the calculation with the 
highest cutoff. I can also extract the corresponding total force or stress.


Finally, I definitely agree with you about the "hardness" of 
pseudo-generation; the results I was reporting are from the checks on 
the SSSP pseudos (or pslibrary v 0.1<->1.0.0 ones, in general, which 
yield similar numbers), the only difference lies in taking into account 
a system more complex that a single atom. In my particular case, I did 
consider a small patch of graphene-like C,N compound.


Hence I wondered if there was any modification, given the possible 
differences between the isolated atom and the small patch, to improve 
the effectiveness of the pseudo (hence, not just hardness, but a proper 
size of the dual). My first guess was to check the transferability of 
the pseudo, which maybe was not enough to cover the electronic 
configuration of the patch. That's what I could not test with ld1.x


Bests,




--
------
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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] [QE users] pseudopotential hardness and transferability

[Nicola Marzari]

On 02/04/2020 18:16, Aldo Ugolotti wrote:

Dear Nicola,

thanks for your reply. I mentioned the energy criteria for convergence 
as the simplest one to verify.


Dear Aldo,

indeed, it is simple, but also it is not relevant, so there aren't many 
conclusions that can be drawn from it.


Regarding the pseudos you mentioned (PBE), those available at the 
materialscloud portal, I have checked them either in the atomic case and 
for a simple system of interest. In the latter case, I found that the 
required minimal cutoffs are ~90/225 Ry while in the former case the 
results of ld1.x (for Hamiltonian evaluation with Bessel functions) are 
consistent with the numbers you reported.


For the SSSP, the cutoffs are based on convergence of phonon 
frequencies, stress, and formation energies; the systems considered are 
the elemental solids of Cottonier (we have protocols also for more 
complex systems). Of course, you might need tighter cutoffs for your 
goals, or you could afford looser ones. Not sure what your tests are, 
but a cutoff of 90/225 (i.e. a dual of 2.5) is quite unusual - the 
charge density would need a dual of 4 for a norm-conserving 
pseudopotential (admittedly, once could use a bit less) but the ones you 
are testing are not even norm-conserving, but PAW or ultrasoft, where 
duals in the range 6-16 are common (for C and N, you might get away with 
something like 6).


Generating pseudopotentials that are softer while remaining accurate is 
exceedingly difficult, as you can see from the literature.



If I understood correctly the works you referred to, the delta parameter 
seems much more large-scale (i.e. code to code) than the scope I am 
working in, as I am not validating a pseudo generation procedure, (which 
I am assuming to be already accurate, given the source) but rather I am 
trying to understand the system-dependency of the behavior of the 
pseudo. However, I am mistaken, I will be glad to check those papers 
again and run some tests.


The delta parameter checks if the equation of state of an elemental 
solid described with a pseudopotential is similar to the all electron 
calculations of the same solid.


nic


--
--
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Director, National Centre for Competence in Research NCCR MARVEL, EPFL
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Re: [QE-users] [QE users] pseudopotential hardness and transferability

[Nicola Marzari]

)    De AE-PS (Ry)
  1 0 2S   1( 2.00)   -0.62966   -0.17919 -0.45046  !
  2 1 2P   1( 3.00)   -0.02904   -0.0 -0.02904  !

  eps = 3.2E-04  iter =201

  Etot = -78.638531 Ry, -39.319266 Ha,   -1069.931632 eV
  Etotps =   -18.974270 Ry,  -9.487135 Ha,    -258.158068 eV
  dEtot_ae =  -3.108582 Ry
  dEtot_ps =  -1.208418 Ry,   Delta E=  -1.900164 Ry

  Ekin =  10.222924 Ry,   5.111462 Ha, 139.089950 eV
  Encl = -31.022876 Ry, -15.511438 Ha,    -422.087699 eV
  Ehrt =  12.620743 Ry,   6.310371 Ha, 171.713935 eV
  Ecxc = -10.795060 Ry,  -5.397530 Ha,    -146.874254 eV
  (Ecc =  -0.958640 Ry,  -0.479320 Ha, -13.042955 eV)

  -- End of pseudopotential test 
--



  -- Test with a basis set of Bessel functions --

  Box size (a.u.) :   30.0

  Cutoff (Ry) :   30.0
    N = 1   N = 2   N = 3
  E(L=0) =    -0.1788 Ry    0.1213 Ry    0.1854 Ry
  E(L=1) = 0.1263 Ry    0.1949 Ry    0.2715 Ry

  Cutoff (Ry) :   60.0
    N = 1   N = 2   N = 3
  E(L=0) =    -0.1789 Ry    0.1213 Ry    0.1854 Ry
  E(L=1) = 0.1263 Ry    0.1949 Ry    0.2715 Ry

  Cutoff (Ry) :   90.0
    N = 1   N = 2   N = 3
  E(L=0) =    -0.1789 Ry    0.1213 Ry    0.1854 Ry
  E(L=1) = 0.1263 Ry    0.1949 Ry    0.2715 Ry

  Cutoff (Ry) :  120.0
    N = 1   N = 2   N = 3
  E(L=0) =    -0.1789 Ry    0.1213 Ry    0.1854 Ry
  E(L=1) = 0.1263 Ry    0.1948 Ry    0.2715 Ry

  -- End of Bessel function test 


Thank you in advance,




--
----------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] Issue with highest frequency optical band phonons at gamma point in GaN

[Nicola Marzari]

On 24/03/2020 23:54, Baer, Bradly wrote:

Nicola,

The image is in the outputs folder as "gan.phonons.bands.ps" That is the 
native output from the plotbands.x code as far as I know.  It is 
possible that it has been slow to finish uploading from my computer to 
the google drive though.


Thanks - it's there now, but it wasn't before - there were much fewer 
files. Anyhow, the LO-TO splitting is exactly the issue. Plenty of 
literature, but start from that listed.


nicola





I will take a look at the links you provided and I appreciate you taking 
the time to write your reply.


Thanks,
Brad


Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University


----
*From:* Nicola Marzari 
*Sent:* Tuesday, March 24, 2020 5:36 PM
*To:* Quantum ESPRESSO users Forum ; 
Baer, Bradly 
*Subject:* Re: [QE-users] Issue with highest frequency optical band 
phonons at gamma point in GaN



Dear Bradly,

without seeing the image (wasn't there in the google folder) the obvious
guess is that phonons in polar materials require a special treatment -
maybe have a look at
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.aps.org%2Fprb%2Fabstract%2F10.1103%2FPhysRevB.43.7231&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cf6d82383087c4065e82a08d7d043c71f%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637206861856438833&sdata=Gj4zzJGY%2F4QRFV6oBN83EmExNE%2F4LNuH3O7RgByRyFA%3D&reserved=0 
or

https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjournals.aps.org%2Frmp%2Fabstract%2F10.1103%2FRevModPhys.73.515&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cf6d82383087c4065e82a08d7d043c71f%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637206861856438833&sdata=neMQPei1nhq7HnGSESWkLMzfvGC6bJ2XZP3l3U9Qtig%3D&reserved=0

A summary by Paolo Giannozzi on using PHonon is here:
https://nam04.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.fisica.uniud.it%2F~giannozz%2FQE-Tutorial%2F&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cf6d82383087c4065e82a08d7d043c71f%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637206861856448828&sdata=BMa2Mv%2Fr2wT9iCutYqRRcMugfMEBkvJTUAj9LKjXOxw%3D&reserved=0

     nicola



On 24/03/2020 23:27, Baer, Bradly wrote:

Hello everyone,

I am attempting to generate the phonon dispersion plot for ZincBlende 
GaN.  The highest frequency optical band of the dispersion is producing 
the wrong result at the gamma point.  The rest of the dispersion looks 
correct for the most part.  Below is a link to a google drive folder 
with a copy of my current input and output files.  It also has an image 
of the dispersion as plotted by plotbands.x.  I also tried the same 
calculation in SiC and saw the same issue at the gamma point (both are 
FCC).  Am I doing something incorrectly that would cause an issue at the 
gamma point only?  I appreciate any advice on the matter.


https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13WDzUBL3DNwasxsDR1gz47MIDh8LtMLZ&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cf6d82383087c4065e82a08d7d043c71f%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637206861856448828&sdata=%2BhHaIluljELkLOzsNDmP%2F2YfhboZrcCUGdBv7XhrCPc%3D&reserved=0

Thanks,
Brad


Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University



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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftheossrv1.epfl.ch%2FMain%2FContact&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Cf6d82383087c4065e82a08d7d043c71f%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637206861856448828&sdata=ZaLgwwXbWsRrttalzyKTgkUWYo6fdJ9lFxAMnZKDPHk%3D&reser

Re: [QE-users] Issue with highest frequency optical band phonons at gamma point in GaN

[Nicola Marzari]

Dear Bradly,

without seeing the image (wasn't there in the google folder) the obvious 
guess is that phonons in polar materials require a special treatment - 
maybe have a look at 
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.43.7231 or 
https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.73.515


A summary by Paolo Giannozzi on using PHonon is here:
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/

nicola



On 24/03/2020 23:27, Baer, Bradly wrote:

Hello everyone,

I am attempting to generate the phonon dispersion plot for ZincBlende 
GaN.  The highest frequency optical band of the dispersion is producing 
the wrong result at the gamma point.  The rest of the dispersion looks 
correct for the most part.  Below is a link to a google drive folder 
with a copy of my current input and output files.  It also has an image 
of the dispersion as plotted by plotbands.x.  I also tried the same 
calculation in SiC and saw the same issue at the gamma point (both are 
FCC).  Am I doing something incorrectly that would cause an issue at the 
gamma point only?  I appreciate any advice on the matter.


https://drive.google.com/open?id=13WDzUBL3DNwasxsDR1gz47MIDh8LtMLZ

Thanks,
Brad


Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University



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--
--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
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] how to study adsorption energy (Sydney Liu)

[Nicola Marzari]

_m_MOD_xc_f03_func_info_get_n_ext_params'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:721: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_init'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:722: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:723: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_info_get_n_ext_params'
 > /home/arini/Downloads/QE/q-e-qe-6.5/Modules/funct.f90:724: undefined
 > reference to `__xc_f03_lib_m_MOD_xc_f03_func_end'
 > collect2: error: ld returned 1 exit status
 > Makefile:256: recipe for target 'pw.x' failed
 > make[2]: *** [pw.x] Error 1
 > make[2]: Leaving directory
'/home/arini/Downloads/QE/q-e-qe-6.5/PW/src'
 > Makefile:9: recipe for target 'pw' failed
 > make[1]: *** [pw] Error 1
 > make[1]: Leaving directory '/home/arini/Downloads/QE/q-e-qe-6.5/PW'
 > Makefile:74: recipe for target 'pw' failed
 > make: *** [pw] Error 1
 >
 > I am not able to find a solution to the problem. I request you to
help me
 > with suggestions and possible corrections to overcome the error.
 >
 > Regards
 > Arini Kar
 > PhD scholar
 > Indian Institute of Technology Bombay
 > India
 > ___
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Message: 2
Date: Sun, 1 Mar 2020 22:09:34 +0900
From: Christoph Wolf 
To: Quantum Espresso users Forum mailto:users@lists.quantum-espresso.org>>
Subject: Re: [QE-users] how to study adsorption energy
Message-ID:


<mailto:camc_g_52nozxvtew6bucu0dlkh5utnmf2ygp1mesut94_cb...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Dear Sydney,

the following tools are very convenient to build surface slabs with
adsorbates as you described:

http://hjkgrp.mit.edu/content/molsimplify-tutorial-2-slab-builder
https://wiki.fysik.dtu.dk/ase/


If you want to do it more "manually" you can of course also use
Avogadro,
VESTA, or simply a text editor if you have  a lot of time ;)

HTH!
Chris



-- 
Postdoctoral Researcher

Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
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End of users Digest, Vol 152, Issue 2
***

[QE-users] Psi-k 2020 (EPFL, 14-17 Sep 2020)

[Nicola Marzari]

Dear QE Users,


I'm hijacking a bit the list to announce that we have launched the 
registration and put online the program for Psi-k 2020 - this is the 
largest conference worldwide in electronic-structure simulations, with 
140 invited talks, 170 contributed talks (that you can apply for!) and 
39 symposia in 6 parallel sessions.


Two of the plenary speakers are long-established contributors/developers 
of QE and related packages - hence my excuse for posting here :-).


All info at https://www.psik2020.net - official mail below.

Hope to see you in Lausanne!

nicola




Psi-k 2020: Registration is open! (EPFL 14-17 Sep 2020)

*Psi-k 2020 - 14-17 September 2020 - EPFL, Lausanne (Switzerland)*

Dear Psi-k'ers,

This is to announce that the registration for Psi-k 2020 is now open, 
and the full list of invited speakers and symposia is online.


This is the largest event worldwide in first-principles simulations; it 
is held every 5 years (the last two editions, in Berlin in 2010 and in 
San Sebastian in 2015, had more than 1’000 participants each), and with 
7 plenary talks, 140 invited talks, and 170 contributed talks it 
promises to be the most exciting, defining event in the field.


Early-bird deadline is May 1, 2020 – one can register right away, and 
submit an abstract later (by May 1, 2020, to be considered for a 
contributed talk, or by Aug. 1, 2020, for a poster). All information – 
including registration, program, accommodation, and childcare - is 
available at https://www.psik2020.net <https://www.psik2020.net/>.


Looking very much forward to a successful Psi-k 2020, and to seeing you 
all in Lausanne!


Nicola Marzari

Chair, Psi-k Charity and Board of Trustees

*More information: *https://www.psik2020.net <https://www.psik2020.net/>

*The conference*

  * 3.5 days (from 2pm Sept. 14, 2020, to the evening of Sept. 17)
  * 7 plenary talks
  * 39 symposia
  * 6 parallel sessions
  * ~140 invited talks
  * ~170 contributed talks
  * 1 MAD evening to shake it all off!

*Important deadlines*

  * *May 1, 2020* — Early-bird registration deadline *REGISTRATIONS ARE
NOW OPEN! <https://www.psik2020.net/registration>*
  * *May 1, 2020* — Abstract submission deadline to be considered for
contributed oral presentations
  * *May 1, 2020* — Deadline for “Volker Heine Award” applications (to
be advertised soon)
  * *Aug. 1, 2020* — Regular registration deadline
  * *Aug. 1, 2020* — Abstract submission deadline, posters only
  * *Sept. 6, 2020* — Late registration deadline
  * *Sept. 14–17, 2020* — Psi-k 2020 Conference

*Plenary speakers *

  * *Gábor Csányi*, University of Cambridge, UK
  * *Feliciano Giustino*, University of Texas at Austin, USA
  * *Sharon Hammes-Schiffer*, Yale University, USA
  * *Francesco Mauri*, University of Rome Sapienza, Italy
  * *Angelos Michaelides*, University College London, UK
  * *Lucia Reining*, Ecole Polytechnique, France
  * *Nicola Spaldin*, ETH Zurich, Switzerland

*Symposia*

*A | Physical Formalisms*

  * Density and density-matrix functional theories
  * Novel theoretical and computational developments in diagrammatic
many body theory
  * Strong correlations beyond local approximations
  * Open quantum systems and non-adiabatic dynamics
  * Emerging aspects of electron-phonon interactions
  * Strongly correlated materials
  * Exciting core electrons
  * New developments in quantum Monte Carlo simulation
  * Frontiers of DFT and beyond
  * Extreme non-linear optics
  * Excitons in complex materials
  * Non-equilibrium physics
  * New developments in first principles calculations of charge and heat
transport

*B | Algorithms, Software and Data*

  * Recent progress in reduced scaling methods: from quantum chemistry
and DFT to second-principles
  * Statistics and configuration sampling
  * Electrified solid-liquid interfaces
  * Software engineering: libraries for electronic structure applications
  * Machine-learned surrogate models: the quest for ab initio accuracy
at a fraction of the cost
  * Machine learning for many-body quantum physics
  * Structure searching and crystal structure prediction
  * Materials discovery by high-throughput screening and artificial
intelligence
  * Emerging and future computing
  * Current and future challenges associated with data infrastructure
and reproducibility

*C | Applications to Real Materials and Materials Design*

  * Ab initio guided design of structural materials
  * Functional materials and devices
  * Magnetism and spintronics
  * Surfaces and interfaces at realistic conditions
  * New physics in 2D materials and van der Waals multilayers
  * Molecules, macromolecules and biomolecules: challenges and new
opportunities for electronic structure methods
  * Twisted bilayer materials
  * Topological properties in real and momentum space
  * Strong spi