Re: [QE-users] Where to get HGH-NLCC pseudopotential?

[Pietro Davide Delugas]

Hello

They are also at this link:

http://pseudopotentials.quantum-espresso.org/legacy_tables/hartwigesen-goedecker-hutter-pp

Pietro


From: users  on behalf of Nicola 
Marzari via users 
Sent: Tuesday, October 22, 2024 08:23
To: yike.huang ; Quantum ESPRESSO users Forum 
; Yu Jusong ; Pizzi 
Giovanni ; Krack Matthias 
Subject: Re: [QE-users] Where to get HGH-NLCC pseudopotential?


Not sure - some seem to be distributed with the code:
Quick Start - Command Line — BigDFT-suite 1.9.2 
documentation
l_sim.gitlab.io
[cid:2f5092d8-8b51-4fb3-8f69-fff866789f8b]

I also ask Matthias Krack, here in cc - I think they are also distributed with 
CP2K, so we can also update the SSSP pointer.

Nicola

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

On 22 Oct 2024, at 08:12, yike.huang via users 
 wrote:


Dear QE users and developers,

I am performing atomization energy tests with QE and I find HGH-NLCC 
pseudopotentials are tested to be excellent (10.1063/1.4793260). I note that on 
SSSP (Standard Solid State Pseudopotential library, SSSP precision 
(materialscloud.org))
 there are indeed test result of this pseudopotential family, but seems the 
resource 
(http://bigdft.org/Wiki/index.php?title=New_Soft-Accurate_NLCC_pseudopotentials)
 has been removed. Does anyone know where I can download this set of 
pseudopotentials? Thanks pretty much!

Very best wishes,
Yike HUANG

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P
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Re: [QE-users] Large time lag post software upgradation in HPC system

[Pietro Davide Delugas]

Hello
It is strange because qe v7.3 is way faster than 6.7, especially on GPUs. It 
has to do with some fine-tuning in using the cluster.
You should ask help to the system managers of your cluster.
Just trying to guess:

  1.
The problem might be hyperthreading, so make sure that OMP_NUM_THREADS is set 
to 1.
  2.
try to see in the GPU MPI aware communications are working compile with 
--with-cuda-mpi=no

hope it helps
best regards
Pietro

From: users  on behalf of Niharika 
Joshi 
Sent: Tuesday, October 15, 2024 09:34
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] Large time lag post software upgradation in HPC system

Dear QE users,
I am using a HPC resource for more than a year with QE(6.7Max GPU) without any 
issue. My present research problem focuses on studying methane and carbon 
dioxide adsorption on spinel surfaces. The system is large with more than 380 
atoms and ~3500 electrons. Normally, 2-3 ionic cycles (with 60-70 iterations) 
gets complete within a day. However, recently there has been some software 
upgradation in the computing system after which I have observed a huge time lag 
in my calculations. Currently, only few iterations are performed in 24 hours.

Please find below two tables listing the details of hardware specifications and 
upgradation information of software in the computing system.

Component
Specification
CPU
AMD EPYC 7742 64C 2.25GHz
CPU core
128 cores (Dual socket each with 64 cores); 256 cores with hyper-threading
L3 cache
256 Mb
RAM
1 TB
GPU
NVIDIA A100-SXM4
GPU Memory
 40 Gb
Total no. of GPU per node
8
Storage
10.5 PiB PFS based storage
Networking
Mellonex ConnectX-6 VPI (infiniband HDR)


Software
Specification of upgradation
OS
from Ubuntu 20.04.02 (DGX OS 5.0.5) to Ubuntu 22.04.04 (DGX OS 6.3.0)
Kernel
 from 5.4.0-80-generic to 5.15.0-1062-nvidia
CUDA
10.1 to 12.4 (below versions are also available)
NVIDIA Driver version
450.142.00 to 550.90.07

Post software upgradation, QE-7.3 was installed in the following manner:

Step 1 : Source up the HPC-SDK environment:
source /opt/hpc-sdk-23.9/env.sh

Step 2. Set up the environment:
./configure --prefix=installation-location --with-cuda=$CUDA_ROOT 
--with-cuda-runtime=12.2 --with-cuda-cc=80 --enable-openmp --with-scalapack=no 
--with-cuda-mpi=yes

Step 3. Compile the source code:
make all -j8

Step 4. Install the compiled binaries:
make install

Kindly, suggest some solution to this problem. Any advice/suggestion at this 
point would really be very helpful to me.

With best regards,
Niharika Joshi,
National Post Doctoral Fellow,
CSIR National Chemical Laboratory, Pune,
Maharashtra-411008, India.



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Re: [QE-users] Reduced mass?

[Pietro Davide Delugas]

Hello
Generally, the reduced mass of the phonon modes is not very useful because it 
is implicitly included in the normalization of their displacements, and 
introducing it explicitly would only complicate things.
However, one definition of the reduced mass could be:

[cid:adf309ce-e8ba-4316-be5b-240a7f203c74]
Where k is the index running on all atoms, m_k is the mass, and u_k are the 
displacements of the mode.


Here are some notes https://hackmd.io/@pietrodelugas/r1SykO511l
Pietro

From: users  on behalf of Andrii 
Shyichuk via users 
Sent: Saturday, October 12, 2024 01:21
To: users@lists.quantum-espresso.org 
Subject: [QE-users] Reduced mass?

Dear Users,

How do I get the reduced mass of a vibrational (phonon) mode from (I
guess) PH.X?

I assume it must be calculated somewhere, but it is not printed. It is
not mentioned in the PH manual (searched for "mass") and it looks like
nobody asked it here (searched for "reduced mass").

Thank you.

Best regards.

dr Andrii Shyichuk, Faculty of Chemistry, University of Wrocław



dr Andrii Shyichuk
ADIUNKT
Zakład Chemii Nieorganicznej, Wydział Chemii

Uniwersytet Wrocławski
ul. F. Joliot-Curie 14
50-383 Wrocław
tel. +48 71 375 72 65

[cid:2022_02_uwr_arqus_pocitedostopki_bdb4c7bb-1172-4107-90f8-1b2742af358e.png][cid:2022_02_uwr_arqus_pocitedostopki3_e5829564-9e6b-4628-ac3b-6e1d97627e4b.png][cid:2022_02_uwr_arqus_pocitedostopki4_89c9e33b-31a4-4974-a07d-b817a789344c.png]

Wiadomość ta oraz wszelkie załączone do niej pliki są poufne i mogą być prawnie 
chronione. Jeżeli nie jest Pani/Pan zamierzonym adresatem niniejszej 
wiadomości, nie może Pani/Pan jej ujawniać, kopiować, dystrybuować ani też w 
żaden inny sposób udostępniać lub wykorzystywać. O błędnym zaadresowaniu 
wiadomości proszę niezwłocznie poinformować nadawcę i usunąć wiadomość.
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Re: [QE-users] The orbitals of a hydrogen atom

[Pietro Davide Delugas]

Dear Toshiharu

If you compute the ILDOS of a system with spherical symmetry, such as the H 
atom, you should get a spherically symmetric distribution. For example, the 3 p 
orbitals will have the same energy, and when computing the ILDOS in their 
energy span, you will get the contributions of p_x, p_y, and p_z, thus creating 
an isotropic plot.
You may try to get something different, breaking the spherical symmetry, such 
as an atom with partially filled shells. You might find a case like that in the 
pw_atom directory of the QE test suite.

Otherwise, plot the charge density contribution of single orbitals with 
plot_num = 7. An example of this for molecules is here:
https://gitlab.com/pietrodelugas/materials-for-max-qe2021-online-school/-/tree/master/Day-1?ref_type=heads

best regards
Pietro

From: users  on behalf of Toshiharu 
Higuchi via users 
Sent: Friday, October 11, 2024 14:10
To: "'Quantum ESPRESSO users Forum'" ; 
"'ROBERT MIKHAIL GUZMAN ARELLANO'" 
Subject: Re: [QE-users] The orbitals of a hydrogen atom


Dear Professor Robert,

thank you very much for your helpful comment.

According to your explanation, a pseudopotential only reproduces the valence 
states (occupied) and the lowest energy unoccupied states. If you open the 
pseudopotential used in your input file, you will see that it reproduces only 
the *s* and *p* states of hydrogen atoms.

However, in my calculations, the orbit is spherical even in the *p* state.

Could you please tell me the reason for this?



Best regard,

Toshiharu Higuchi



From: ROBERT MIKHAIL GUZMAN ARELLANO 
Sent: Friday, October 11, 2024 5:11 AM
To: toshi1h...@docomo.ne.jp; Quantum ESPRESSO users Forum 

Subject: Re: [QE-users] The orbitals of a hydrogen atom



Dear Toshiharu,

Thank you very much for sharing your input files for pw.x and pp.x.

I believe this might be the information you're looking for regarding how to 
plot a specific Kohn-Sham orbital: https://www.youtube.com/watch?v=FrY8Sj0zUus

On another note, pseudopotentials do not include all atomic orbitals of the 
atoms. A pseudopotential only reproduces the valence states (occupied) and the 
lowest energy unoccupied states. If you open the pseudopotential used in your 
input file, you will see that it reproduces only the s and p states of hydrogen 
atoms. If you are interested in d orbitals, you can use a pseudopotential for 
elements like Nickel or Cobalt.

Best regards,



El mié, 9 oct 2024 a las 20:57, Toshiharu Higuchi via users 
(mailto:users@lists.quantum-espresso.org>>) 
escribió:

Dear members of Quantum-Espresso,
I am a beginner of Quantum-Espresso. My question is about the orbital of a
hydrogen atom. I calculated the orbital of a hydrogen atom using
Quantum-Espresso. The orbitals of the hydrogen atom have already been
analytically solved.  These orbitals are (1) s-orbital is a spherically
symmetric orbital, (2) p-orbitals have two lobes with a node located at the
nucleus, and (3) d-orbitals have two types of orbitals, one kind of orbitals
consist of a cloverleaf shape, with four electron-dense lobes, and another
type of orbital has two lobes oriented in the z-axis with a donut-shaped
ring in the x-y plane.

However, the orbitals obtained with Quantum-Espresso (assuming the ILDOS
pattern as the orbital) were all spherically symmetric orbitals from the
first orbital to the tenth orbital. I was not able to obtain a pattern with
a shape like p-orbital or d-orbital.
Could someone tell me why the orbital turned out like this?

My input data is as follows.

[1] pw.x input
&CONTROL
   title = 'QE_H_atom_Orbital_2' ,
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  wf_collect = .true. ,
  outdir = '/home/user/tmp/' ,
  pseudo_dir =
'/home/user/user/espresso-5.0.1/espresso-5.0.1/pseudo/' ,
  prefix = 'QE_H_atom_Orbital_2' ,
   verbosity = 'high' ,
 tstress = .false. ,
 tprnfor = .false. ,
 tefield = .false. ,
dipfield = .false. ,
lelfield = .false. ,
 /
 &SYSTEM
   ibrav = 8,
   A = 20.0 ,
   B = 20.0 ,
   C = 45.0 ,
 nat = 1,
ntyp = 1,
 ecutwfc = 26 ,
 ecutrho = 156 ,
nbnd = 228,
 occupations = 'smearing' ,
 starting_spin_angle = .true. ,
 degauss = 0.003675 ,
smearing = 'gaussian' ,
   nspin = 1 ,
 nr1 = 36 ,
 /
 &ELECTRONS
electron_maxstep = 2000,
conv_thr = 1.D-6 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.05 ,
 /
ATOMIC_SPECIES
H1.0  H.

Re: [QE-users] QE-GPU Running Error

[Pietro Davide Delugas]

Hello


Usually the "libgomp: TODO" error message occurs because the program has been 
linked with a cuda version that is not compatible with the gpu  driver that is 
running in the nodes.
You should inquire with the system managers of your cluster about the right 
toolchain to use.
Or check the cuda and driver versions and report them in the forum to get more 
help.
Pietro



Il 24 set 2024 7:06 PM, "Hazra, Shilpa"  ha scritto:
Hello,

I am using the cuda version of Quantum Espresso. The input and the job 
submission script I am using are written bellow.


INPUT:

&control
calculation = 'vc-relax'
prefix = 'silicon'
outdir = './tmp/'
pseudo_dir = './'
etot_conv_thr = 1e-5
forc_conv_thr = 1e-4
/

&system
ibrav=2, celldm(1) =14,
nat=2, ntyp=1,
ecutwfc=30
/

&electrons
conv_thr=1e-8
/

&ions
/

&cell
cell_dofree='ibrav'
/

ATOMIC_SPECIES
  Si  28.0855  Si.pbe-n-kjpaw_psl.1.0.0.UPF

ATOMIC_POSITIONS (alat)
  Si 0.00 0.00 0.00 0 0 0
  Si 0.25 0.25 0.25 0 0 0

K_POINTS (automatic)
  6 6 6 1 1 1
~
~
SCRIPT:

#!/bin/bash
#SBATCH --job-name="test2"
#SBATCH --output="test2.out"
#SBATCH --partition=gpuA40x4
#SBATCH --mem=16G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=16   # spread out to use 1 core per numa, set to 64 if 
tasks is 1
#SBATCH --constraint="scratch"
#SBATCH --gpus-per-node=4
#SBATCH --gpu-bind=closest   # select a cpu close to gpu on pci bus topology
#SBATCH --account=bcox-delta-gpu# <- match to a "Project" returned by the 
"accounts" command
#SBATCH -t 08:00:00
#SBATCH -e slurm-%j.err
#SBATCH -o slurm-%j.out

module reset
module load nvhpc/22.11
module load openmpi/4.1.5+cuda
module load quantum-espresso/7.3.1+cuda

export OMP_NUM_THREADS=16  # if code is not multithreaded, otherwise set to 8 
or 16
srun pw.x -N 1 -n 1 test2.in > test2.out

Moreover, the job is running well. But I am not getting any output data printed 
in the output file even after running the job for 30 hours. Along with that, I 
am getting the following error massage in the .err file.

libgomp: TODO
srun: error: gpub075: task 0: Exited with exit code 1

I am really not getting why this error is happening and the error is coming. I 
tried to adjust the script for parallel computing. However, all the time I am 
getting the same error. Please help me out form this problem. If you could help 
me with solving this problem, it would be really beneficial for me.  Thank you.

Sincerely,
Shilpa Hazra
Ph.D., Chemistry, University of Illinois Chicago




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Re: [QE-users] Empty dynamical matrices files

[Pietro Davide Delugas]

Hello
It is hard to say what happened without a look at the outputs. Could you send 
the output of the nq=3,3,3 calculations?
One hypothesis that it is better to check is that you first did the calculation 
with nq =2,2,2 and then the one with nq = 3,3,3 using the same prefix. Because 
recover is set to true, the program could have been detoured by possibly 
preexisting status files it read trying to recover data from the previous 
calculation.

Best regards
Pietro


From: users  on behalf of Soham Ghosh 

Sent: Wednesday, July 10, 2024 23:54
To: users@lists.quantum-espresso.org 
Subject: [QE-users] Empty dynamical matrices files

Hello QE users and experts,

In my phonon calculations, some of the dynamical files seem to not be written, 
even though ph.x runs fine and the calculation is complete. The files are 
created, but are empty. I have tested this with QE-7.3 and QE-7.0. Can you 
kindly help me with understanding why?

My ph.in is as follows:


--

&inputph

  prefix   = 'H3S_270_2x2x2',

  fildyn   = 'H3S_270_2x2x2.dyn',

  amass(1) = 32.065,

  amass(2) = 1.00794,

  outdir   = './'

  ldisp= .true.,

  trans= .true.,

  fildvscf = 'dvscf',

  nq1=3,

  nq2=3,

  nq3=3,

  tr2_ph   =  1.0d-14

  recover = .true.

 /


For (nq1, nq2, nq3) = (2,2,2) I do get meaningful dynamical matrix files.

Best,
Soham Ghosh.
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Re: [QE-users] [SPAM] Convergence problems

[Pietro Davide Delugas]

Hello
a few suggestions:


  1.  The convergence issues you are experiencing may be due to your starting 
configuration; check that it is a sensible one.
  2.
Use a larger smearing, and if you are using an old version of qe, try to switch 
to gauss smearing,
  3.
 Diagonalization='cg' is very slow and inefficient; unless Davidson fails, it 
is better to  stick to that; otherwise

  diagonalization='rmm-davidson' or 'rmm-paro'.

5) If you are not using a recent version of qe ( 7.2 or older ), avoid 
using local-TF because, in some cases, it could lead to practically infinite 
loops. This behaviour has been fixed in qe-7.3.
   6) Interpolating potential and wave functions is not helpful for 
relaxations because steps are generally longer than in dynamics.

 7) conv_thr=10^-6 is a too high threshold to obtain any reliable 
relaxation, it may be good for the very first steps of the relaxation but as 
soon as the forces become small you will need to use a lower threshold at least 
 > 10^-8 to make the relaxation converge.

best regards
Pietro


From: users  on behalf of Janiny 

Sent: Wednesday, July 3, 2024 18:26
To: users@lists.quantum-espresso.org 
Subject: [QE-users] [SPAM] Convergence problems


Dear all,

1) I am conducting an adsorption study, and convergence is taking too long (in 
some cases, over 20 days). Additionally, there are situations where more than 
100 iterations pass without generating coordinates. Is it possible to 
periodically fix the coordinate generation?

2) I am using conv_thr = 10^-6. Do you suggest any other parameters that I 
could adjust to improve convergence?

 &control
  calculation='relax'
wf_collect = .TRUE.
!  restart_mode = 'restart'
  max_seconds = 1.D+10
  disk_io='low'
/
 &system
ibrav = 0, celldm(1) =xxx,nat=xxx, ntyp= xxx,
ecutwfc = 55.0, ecutrho = 600,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01
nspin= xxx
tot_magnetization= xxx
 /
 &electrons
conv_thr = 1.0e-6
mixing_beta = 0.1
mixing_mode= 'local-TF'
electron_maxstep=500
diago_thr_init = 1e-4
diagonalization = 'cg'
/
&ions
ion_dynamics = 'bfgs'
pot_extrapolation = 'second_order'
wfc_extrapolation = 'second_order'


Best regards,
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Re: [QE-users] PHonon regression

[Pietro Davide Delugas]

Hi,
Thanks very much for reporting the issue. We should have it fixed very soon.
Fortunately, it should only affect a few cases when using pseudopotentials 
without any projector.

Pietro

From: users  on behalf of Scott 
Brozell 
Sent: Thursday, June 27, 2024 22:08
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] PHonon regression

Hi,

I am reporting a regression in QE 7.3 for PHonon/examples/example04
which calculates the normal modes of the molecule CH4.
We have typical hardware running various versions of RHELS, eg:
Model name:Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Red Hat Enterprise Linux Server release 7.9 (Maipo)

There is no difference in the total energies from ch4.scf.out.
For a build with intel 19.0.5 (including mkl) and mvapich2 2.3.3
the frequencies in ch4.nm.out are initially all asterisks, but after
a minor change:
(
diff q-e-qe-7.3/PHonon/PH/dyndia.f90 q-e-qe-7.3formatchange/PHonon/PH/dyndia.f90
96c96
< 9010 format   (5x,'freq (',i5,') =',f15.6,' [THz] =',f15.6,' [cm-1]')
---
> 9010 format   (5x,'freq (',i5,') =',g15.6,' [THz] =',g15.6,' [cm-1]')
)
the frequencies are seen to be astronomical:
 **
 freq (1) =  -0.479981+102 [THz] =  -0.160105+104 [cm-1]
 freq (2) =  -0.206365+102 [THz] =  -0.688359+103 [cm-1]
 freq (3) =  -0.192288+102 [THz] =  -0.641402+103 [cm-1]
 freq (4) =  -0.174235+102 [THz] =  -0.581187+103 [cm-1]
 freq (5) =  -0.124589+102 [THz] =  -0.415585+103 [cm-1]
 freq (6) =  -0.621996+101 [THz] =  -0.207476+103 [cm-1]
 freq (7) =  -0.599140+101 [THz] =  -0.199851+103 [cm-1]
 freq (8) =  -0.137753E+94 [THz] =  -0.459496E+95 [cm-1]
 freq (9) =   0.294112E+94 [THz] =   0.981053E+95 [cm-1]
 freq (   10) =   0.195386+101 [THz] =   0.651739+102 [cm-1]
 freq (   11) =   0.455999+101 [THz] =   0.152105+103 [cm-1]
 freq (   12) =   0.644921+101 [THz] =   0.215123+103 [cm-1]
 freq (   13) =   0.343296+102 [THz] =   0.114511+104 [cm-1]
 freq (   14) =   0.346276+102 [THz] =   0.115505+104 [cm-1]
 freq (   15) =   0.421103+102 [THz] =   0.140465+104 [cm-1]
 **

For a qe7.3 build with gnu 8.4.0, mvapich2 2.3.3, and mkl 2019.0.5
the frequencies in ch4.nm.out are merely bad:
 **
 freq (1) =  -9.773705 [THz] =-326.015720 [cm-1]
 freq (2) =  -8.889882 [THz] =-296.534532 [cm-1]
 freq (3) =  -5.549399 [THz] =-185.108021 [cm-1]
 freq (4) =   1.585071 [THz] =  52.872283 [cm-1]
 freq (5) =   5.255137 [THz] = 175.292486 [cm-1]
 freq (6) =   6.649912 [THz] = 221.817198 [cm-1]
 freq (7) =  34.550754 [THz] =1152.489094 [cm-1]
 freq (8) =  37.202830 [THz] =1240.952824 [cm-1]
 freq (9) =  37.503239 [THz] =1250.973413 [cm-1]
 freq (   10) =  43.470790 [THz] =1450.029471 [cm-1]
 freq (   11) =  43.472451 [THz] =1450.084874 [cm-1]
 freq (   12) =  89.328051 [THz] =2979.663039 [cm-1]
 freq (   13) =  90.261402 [THz] =3010.796276 [cm-1]
 freq (   14) =  92.248874 [THz] =3077.091230 [cm-1]
 freq (   15) =  94.624278 [THz] =3156.326165 [cm-1]
 **

Note that the reference outputs are from v.6.0, but we have had
consistent agreement through 6.7.  7.3 is the first v7 we've installed.
This smells fishy even though it is only a toy calculation,
but i wanted to notify the community and get feedback before
submitting a gitlab issue.

Best regards,

Scott

--
Scott Brozell, Ph.D.
Scientific Applications Senior Engineer
Scientific Applications Group
Ohio Supercomputer Center
1224 Kinnear Rd.
Columbus, OH 43212

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Quant

Re: [QE-users] QE installation error with gpu

[Pietro Davide Delugas]

Hello
Try with CC=nvc, nvcc is the cuda  compiler

Il 28 giu 2024 4:20 PM, sj...@sejong.edu ha scritto:
Hi all,
I am new to QE. I am trying to install QE with GPU.  I installed nvidia hpc_sdk 
v.24.5 for this on
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5
My gpu is Geforce RTX 3080 (Ampere architecture I suppose).

After successful (?) configure command, I made "make all" and I got following 
error.
To me, it seems nvcc compiler doesn’t take '-gpu=cc80,cuda12.4' option.

In fact,
$ which nvcc
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4/bin/nvcc
$ nvcc -gpu=cc80,cuda12.4
nvcc fatal   : Unknown option '-gpu=cc80,cuda12.4'

I might be wrong though.

Any advice or help will be greatly apprecited.
Thank you very much in advance.
SJ

$make all
make[1]: Entering directory `/home/sjang/install/qe-7.3.1/UtilXlib'
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA -D__DFTI 
-D__MPI -D__SCALAPACK  -cuda -gpu=cc80,cuda12.4 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src 
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I. -c 
parallel_include.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA -D__DFTI 
-D__MPI -D__SCALAPACK  -cuda -gpu=cc80,cuda12.4 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src 
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I. -c 
util_param.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA -D__DFTI 
-D__MPI -D__SCALAPACK  -cuda -gpu=cc80,cuda12.4 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src 
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I. -c 
clib_wrappers.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA -D__DFTI 
-D__MPI -D__SCALAPACK  -cuda -gpu=cc80,cuda12.4 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src 
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I. -c 
nvtx_wrapper.f90
/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 -fast -Mcache_align -Mpreprocess -Mlarge_arrays -D__PGI -D__CUDA -D__DFTI 
-D__MPI -D__SCALAPACK  -cuda -gpu=cc80,cuda12.4 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src 
-I/home/sjang/install/qe-7.3.1//external/devxlib/include -acc 
-I/home/sjang/install/qe-7.3.1//external/devxlib/src -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include -I. -c 
clocks_handler.f90
nvcc -O3 -D__PGI -D__CUDA -D__DFTI -D__MPI -D__SCALAPACK -I. 
-I/home/sjang/install/qe-7.3.1//include 
-I/usr/local/intel/compilers_and_libraries_2020.4.304/linux/mkl/include 
-gpu=cc80,cuda12.4 -acc  -c cptimer.c
nvcc fatal   : Unknown option '-gpu=cc80,cuda12.4'
make[1]: *** [cptimer.o] Error 1
make[1]: Leaving directory `/home/sjang/install/qe-7.3.1/UtilXlib'
make: *** [libutil] Error 1

--
Before ‘make all’ command, this is my configure command and resulting log

$echo $NVHPC_CUDA_HOME
/opt/nvidia/hpc_sdk/Linux_x86_64/2024/cuda/12.4

$./configure F90=nvfortran 
MPIF90=/opt/nvidia/hpc_sdk/Linux_x86_64/24.5/comm_libs/12.4/openmpi4/openmpi-4.1.5/bin/mpif90
 CC=nvcc CXX=nvc++ --with-cuda=$NVHPC_CUDA_HOME --prefix=$HOME/QE 
--with-cuda-cc=80 --with-cuda-runtime=12.4

….
….
all dependencies updated successfully
checking build system type... x86_64-pc-linux-gnu
checking ARCH... x86_64
checking setting AR... ... ar
checking setting ARFLAGS... ... ruv
checking whether the Fortran compiler works... yes
checking for Fortran compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... no
checking whether /opt/nvidia/hpc_sdk/Linux_x86_64/24.5/compilers/bin/nvfortran 
accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking for 
/opt/nvidia/hpc_sdk/Linux_x86

Re: [QE-users] pp.x caused an error when treating hdf5 files

[Pietro Davide Delugas]

Dear Halsten
The type of file where charge density is saved does not depend on its size but 
on how pw.x has been compiled.

I assume that you are using two different executables. Are these both 7.3.1 
versions?

The error occurs when reading the XML file, and in rare cases, the different 
versions may be incompatible.
If you send me the XML file ( it is called data-file-schema.xml and is inside 
the .save directory ), I will try to understand
the issue.

Thanks and best regards
Pietro

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Re: [QE-users] Where can I get the QE-7.0 instalation package while the QE website is not working?

[Pietro Davide Delugas]

The website is back online, you can download the tarball.


From: users  on behalf of Paolo 
Giannozzi 
Sent: Thursday, January 18, 2024 11:34
To: Quantum ESPRESSO users Forum 
Subject: Re: [QE-users] Where can I get the QE-7.0 instalation package while 
the QE website is not working?

There is a temporary problem on the web site

Paolo

On 1/18/24 10:42, Piotr Szkudlarek wrote:
>
> Non si ricevono spesso messaggi di posta elettronica da
> p.szkudla...@cent.uw.edu.pl. Informazioni sul perché è importante
> 
>
>
> Dear Community,
> I want to ask you where I can find the QE 7.0 installation package. At
> the moment, when I am trying to download it, I see that the QE website
> has problems with the database. Is there any alternative way to get that
> package?
> Greetings,
> Piotr Szkudlarek
>
> ___
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> ___
> Quantum ESPRESSO is supported by MaX 
> (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
___
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Re: [QE-users] Convergence issue in spin-polarized SCAN calculation

[Pietro Davide Delugas]

Dear Jing Lian Ng

We finished the release just before the holidays, and the package will be soon 
available on the website .

Pietro


On 27/12/23 08:34, Jing Lian Ng wrote:
Hello Dr Delugas,

Pardon me if I am not replying to the thread correctly. I checked the QE 
homepage and the latest release was only up to v7.2. Did you know where can I 
compile QE v7.3?

Thank you and best regards,
Jing Lian Ng
2nd Year PhD Student at University of Texas

On Mon, Dec 25, 2023 at 7:51 AM Jing Lian Ng 
mailto:jingl...@utexas.edu>> wrote:
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] Convergence issue in spin-polarized SCAN calculation

[Pietro Davide Delugas]

Dear Jing Lian


We recently made a change in the routine that mixes the kinetic energy density 
for the spin polarized case. This improves significantly the convergence of 
metaGGA spin polarized calculations, it is available in the new qe release 7.3 
( the tag has just been done in the repository).
Could you try whether these changes fix your convergence issue?
Thanks and best regards
Pietro




Il 25 dic 2023 2:52 PM, Jing Lian Ng  ha scritto:
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] Error in routine scale_h (1): Not enough space allocated for radial FFT...

[Pietro Davide Delugas]

Hello
This happens when the volume of the cell changes too much during the relaxation.

The best route would be to input the values of the in-plane lattice constant as 
close to real ones as possible, being this a 2D material, to avoid any 
relaxation along the z direction.  This can be done by adding the
cell_dofree='2dxy'
in the &cell namelist
hope this helps
best regards
Pietro

Fvalues ofrom: users  on behalf of 
Dr. Pabitra Mandal 
Sent: Thursday, December 14, 2023 15:30
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] Error in routine scale_h (1): Not enough space allocated 
for radial FFT...

Dear All,
I was doing vc-relax of a carbon based 2D system with 12 carbon atoms. The 
program ran and stopped after giving an error message following:


 Error in routine scale_h (1):
 Not enough space allocated for radial FFT: try restarting with a larger 
cell_factor.
 

 stopping ...

I did not have 'cell_factor' in the input file. I restarted vc_relax with 
lattice parameter larger than the expected actual cell. But I got the same 
error again.

Please help...


From: users  on behalf of Dr. Pabitra 
Mandal 
Sent: Thursday, December 14, 2023 15:30
To: Quantum ESPRESSO users Forum 
Subject: [QE-users] Error in routine scale_h (1): Not enough space allocated 
for radial FFT...

Dear All,
I was doing vc-relax of a carbon based 2D system with 12 carbon atoms. The 
program ran and stopped after giving an error message following:


 Error in routine scale_h (1):
 Not enough space allocated for radial FFT: try restarting with a larger 
cell_factor.
 

 stopping ...

I did not have 'cell_factor' in the input file. I restarted vc_relax with 
lattice parameter larger than the expected actual cell. But I got the same 
error again.

Please help...
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Re: [QE-users] Guidance Required for modelling CaCO3

[Pietro Davide Delugas]

Hello
It might be a problem reading one of the pseudopotential files. Could you check 
that they are regularly terminated?

From: users  on behalf of Saiyed 
Tasnim Md Fahim 
Sent: Wednesday, December 13, 2023 01:49
To: users@lists.quantum-espresso.org 
Subject: [QE-users] Guidance Required for modelling CaCO3

Dear QE users,
I am trying to model the Calcite structure for adsorption study in quantum 
espresso. I am getting the following error:

At line 813 of file xmltools.f90

Fortran runtime error: End of file


I have used the following input file:

&CONTROL

calculation = 'scf'

etot_conv_thr = 3.00d-04

forc_conv_thr = 1.00d-04

outdir = './.'

prefix = 'calcite2'

pseudo_dir = './.'

tprnfor = .true.

tstress = .true.

verbosity = 'high'

/



&SYSTEM

degauss = 1.4699723600d-02

ecutrho = 4.00d+02

ecutwfc = 5.00d+01

ibrav = 0

nat = 30

nosym = .false.

ntyp = 3

occupations = 'smearing'

smearing = 'cold'

/



&ELECTRONS

conv_thr = 6.00d-09

electron_maxstep = 80

mixing_beta = 4.00d-01

/



ATOMIC_SPECIES

C 12.0107 C.pbesol-n-kjpaw_psl.1.0.0.UPF

Ca 40.078 Ca.rel-pbesol-spn-kjpaw_psl.1.0.0.UPF

O 15.9994 O.pbesol-n-kjpaw_psl.1.0.0.UPF



ATOMIC_POSITIONS crystal

Ca 0.00 0.666700 0.166700
Ca 0.00 0.00 0.00

Ca 0.00 0.00 0.50

Ca 0.666700 0.00 0.00

Ca 0.666700 0.00 0.833300

Ca 0.00 0.666700 0.666700

C 0.666700 0.00 0.083300

C 0.00 0.00 0.25

C 0.00 0.666700 0.416700

C 0.666700 0.00 0.583300

C 0.00 0.00 0.75

C 0.00 0.666700 0.916700

O 0.666700 0.0755010400 0.083300

O 0.9244989600 0.5911656200 0.083300

O 0.2578322900 0.00 0.25

O -0.00 0.2578322900 0.25

O 0.7421677100 0.7421677100 0.25

O 0.4088343800 0.00 0.083300

O 0.00 0.4088343800 0.416700

O 0.5911656200 0.9244989600 0.416700

O 0.9244989600 0.00 0.583300

O 0.666700 0.5911656200 0.583300

O 0.4088343800 0.0755010400 0.583300

O 0.0755010400 0.666700 0.416700

O 0.00 0.7421677100 0.75

O 0.2578322900 0.2578322900 0.75

O 0.5911656200 0.666700 0.916700

O 0.00 0.9244989600 0.916700

O 0.0755010400 0.4088343800 0.916700

O 0.7421677100 0.00 0.75



K_POINTS automatic

8 8 2 0 0 0



CELL_PARAMETERS angstrom

5.0068012800   0.00   0.00

-2.5034006400  4.3360171002   0.00

0.00   0.00  16.9901279000


I generated the input file from the pwscf input generator as a starting point. 
Does anyone know how to solve the problem?


Sincerely,
Saiyed Tasnim Md Fahim,
Ph.D. Student,
Environmental Engineering,
University of Southern California.
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[QE-users] R: one question about the matrix element calculation

[Pietro Davide Delugas]

Hi there,

The data in p_avg.dat are k-resolved, which means that point-wise, the 
symmetries are limited to the small group of rotations that preserve the 
specific k-point. However, you can still compare the matrix elements at two 
corresponding rotated k-points.

If your bands are degenerate due to symmetry, it is also necessary to compare 
the correct corresponding partners of the occupied and unoccupied irreducible 
representations.

Hope it helps
Pietro

Da: users  per conto di Yu, Jingjing 

Inviato: domenica 17 settembre 2023 19:01
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] one question about the matrix element calculation

Dear QE community members,

I am a beginner to do the DFT calculation. I have one question regarding
to extracting matrix elements of the momentum operator between the
valence and conduction bands wrriten in the file of "p_avg.dat".

I am wondering if the corresponding matrix elements along the x, y, z
directions should be that same if the crystal structure of material is
cubic (isotropic)?

Thanks a lot!

Best regards,
Jingjing Yu

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[QE-users] R: QE compilation for Mac with Intel processor

[Pietro Davide Delugas]

It looks like a problem with the initialization of the MPI library.

Try to compile a toy program with mpif90 and see if it runs with 2 or more 
ranks.

Pietro


Da: users  per conto di Kliavinek, 
Sergei 
Inviato: mercoledì 13 settembre 2023 19:17
A: Quantum ESPRESSO users Forum 
Oggetto: [QE-users] QE compilation for Mac with Intel processor

Dear QE developers,

I compile QE inside Docker, which I run on several computers, including a Mac 
with an Intel processor. I manage to configure and compile pw.x, however, I get 
the following on running it:

forrtl: severe (168): Program Exception - illegal instruction
Image  PCRoutineLineSource
libc.so.6  7F8B5581A520  Unknown   Unknown  Unknown
libmpi.so.12.0.0   7F8B565EE77F  MPL_wtime_initUnknown  Unknown
libmpi.so.12.0.0   7F8B565DDDFA  MPL_dbg_pre_init  Unknown  Unknown
libmpi.so.12.0.0   7F8B55EA1315  Unknown   Unknown  Unknown
libmpi.so.12.0.0   7F8B55EA0D1B  MPI_Init  Unknown  Unknown
libmpifort.so.12.  7F8B574EC85B  PMPI_INIT Unknown  Unknown
pw.x   00AAD538  Unknown   Unknown  Unknown
pw.x   00AACFF6  Unknown   Unknown  Unknown
pw.x   00407AB5  Unknown   Unknown  Unknown
pw.x   00407A5D  Unknown   Unknown  Unknown
libc.so.6  7F8B55801D90  Unknown   Unknown  Unknown
libc.so.6  7F8B55801E40  __libc_start_main Unknown  Unknown
pw.x   00407975  Unknown   Unknown  Unknown

Here is the configuration command I am using:

./configure CFLAGS=-O3 FFLAGS=-O3 F90=ifort MPIF90=mpiifort 
--with-hdf5="/opt/hdf5"
I've also tried to add arguments  -host=mac686, ARCH="mac686", and this command:
./configure CFLAGS=-O3 FFLAGS=-O3

But also obtained the same result.

However, If directly disable parallelizaton:

./configure CFLAGS=-O3 FFLAGS=-O3 --disable-parallel

Everything works fine.
What could be the problem?

P.S. I use intel toolkit as a base image:
FROM intel/oneapi-hpckit:2023.0.0-devel-ubuntu22.04

Best,
Sergei
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[QE-users] R: R: QE 7.2 compilation with new Intel compilers

[Pietro Davide Delugas]

arallel private(ia, is, iv, jv, rsum_v) reduction (+:rsum) vector_length(32) &

--^

gram.f90(155): error #5082: Syntax error, found '+' when expecting one of: 


 parallel private(ia, is, iv, jv, rsum_v) reduction (+:rsum) vector_length(32) &

-^

gram.f90(157): error #5082: Syntax error, found IDENTIFIER 'GANG' when 
expecting one of: ( : % [ . = =>

 loop gang

--^

gram.f90(164): error #5082: Syntax error, found IDENTIFIER 'VECTOR' when 
expecting one of: ( : % [ . = =>

 loop vector collapse(2) reduction(+:rsum_v)

--^

gram.f90(164): error #5082: Syntax error, found IDENTIFIER 'REDUCTION' when 
expecting one of: :: ) ( , : *  ; . % (/ + - [ ] /) . = ' ** 
/ ...

 loop vector collapse(2) reduction(+:rsum_v)

-^

gram.f90(176): error #5082: Syntax error, found IDENTIFIER 'PARALLEL' when 
expecting one of:  ; TYPE MODULE FUNCTION SUBROUTINE 
PROCEDURE BLOCK DO FORALL ...

 end parallel

-^

gram.f90(177): error #5082: Syntax error, found 'DATA' when expecting one of: 
 ; TYPE MODULE FUNCTION SUBROUTINE PROCEDURE BLOCK DO FORALL 
...

 end data

-^

gram.f90(216): error #5082: Syntax error, found IDENTIFIER 'PRESENT' when 
expecting one of: ) ( , :  ; % [ . = / =>

 & present(ibgrp_g2l, nh, ofsbeta, qq_nt, ityp, tvanp, betae)

---^

gram.f90(216): error #5082: Syntax error, found END-OF-STATEMENT when expecting 
one of: :

 & present(ibgrp_g2l, nh, ofsbeta, qq_nt, ityp, tvanp, betae)

---^

gram.f90(217): error #5082: Syntax error, found IDENTIFIER 'PRESENT' when 
expecting one of: ( : % [ . = =>

 kernels present(csc)

-^

gram.f90(219): error #5082: Syntax error, found IDENTIFIER 'KERNELS' when 
expecting one of:  ; TYPE MODULE FUNCTION SUBROUTINE 
PROCEDURE BLOCK DO FORALL ...

 end kernels

-^

gram.f90(221): error #5082: Syntax error, found IDENTIFIER 'PRESENT' when 
expecting one of: ( : % [ . = =>

 kernels present(cp_tmp)

-^

gram.f90(227): error #5082: Syntax error, found IDENTIFIER 'KERNELS' when 
expecting one of:  ; TYPE MODULE FUNCTION SUBROUTINE 
PROCEDURE BLOCK DO FORALL ...

 end kernels

-^

/tmp/ifx0955286960Qlmjed/ifxwhM11h.i90(236): catastrophic error: Too many 
errors, exiting

compilation aborted for gram.f90 (code 1)

make[2]: *** [../../make.inc:16: gram.o] Error 1

make[2]: Leaving directory '/opt/q-e-qe-7.2/CPV/src'

make[1]: *** [Makefile:7: all] Error 1

make[1]: Leaving directory '/opt/q-e-qe-7.2/CPV'

make: *** [Makefile:75: cp] Error 1



As far as I understand, the compiler is signaling that a large number of syntax 
errors have been caused, which is strange because in that case the code would 
not compile with other compilers. Could you please advise what could be the 
issue?


Best,

Sergei


23 авг. 2023 г., в 2:51 AM, Pietro Davide Delugas  
написал(а):

Hello

tried with Intel suite version 2023.2 this morning, and it works for me.

There may be a slight problem in the configuration though. The configure script 
recognizes that the  compiler is intel and sets in the make.inc F90=ifort 
instead of F90=ifx, which may be the cause of your problems. But  I set F90=ifx 
manually in the make.inc.  before compiling, and I haven't checked what happens 
otherwise.

hope it helps
Pietro

Da: users  per conto di Kliavinek, 
Sergei 
Inviato: martedì 22 agosto 2023 21:34
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] QE 7.2 compilation with new Intel compilers

Dear QE developers,

I am currently working on compiling QE using the new Intel compilers. My 
compile command is as follows:

wget https://github.com/QEF/q-e/archive/refs/tags/qe-7.2.zip && \
unzip qe-7.2.zip && \
cd q-e-qe-7.2 && \
./configure F90=ifx CC=mpiicx CFLAGS=-O3 FFLAGS=-O3 MPIF90=mpiifx  
--with-hdf5="/opt/hdf5" --enable-wannier90 && \
make all && \
rm ../qe-7.2.zip

Unfortunately, I get an error when I run it:

1117.3 mbdlib.f90(26): error #7002: Error in opening the compiled module file.  
Check INCLUDE paths.   [MBD]
1117.3   USE mbd,  ONLY : mbd_input_t, mbd_calc_t
1117.3 --^
1117.3 mbdlib.f90(40): error #6406: Conflicting attributes or multiple 
declaration of name.   [MBD_INPUT_T]
1117.3   TYPE(mbd_input_t):: inp
1117.3 ---^
1117.3 mbdlib.f90(41): error #6406: Conflicting attributes or multiple 
declaration of name.   [MBD_CALC_T]
1117.3   TYPE(mbd_calc_t):: calc
1117.3 ---^
1117.3 mbdlib.f90(26): error #6580: Name in only-list does not exist or is not 
accessible.   [MBD_INPUT_T]
1117.3   USE mbd,  ONLY : mbd_input_t, mbd_calc_t
1117.3 ---^
1117.3 mbdlib.f90(26): error #6580: Name in o

[QE-users] R: QE 7.2 compilation with new Intel compilers

[Pietro Davide Delugas]

Hello

tried with Intel suite version 2023.2 this morning, and it works for me.

There may be a slight problem in the configuration though. The configure script 
recognizes that the  compiler is intel and sets in the make.inc F90=ifort 
instead of F90=ifx, which may be the cause of your problems. But  I set F90=ifx 
manually in the make.inc.  before compiling, and I haven't checked what happens 
otherwise.

hope it helps
Pietro

Da: users  per conto di Kliavinek, 
Sergei 
Inviato: martedì 22 agosto 2023 21:34
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] QE 7.2 compilation with new Intel compilers

Dear QE developers,


I am currently working on compiling QE using the new Intel compilers. My 
compile command is as follows:

wget https://github.com/QEF/q-e/archive/refs/tags/qe-7.2.zip && \

unzip qe-7.2.zip && \

cd q-e-qe-7.2 && \

./configure F90=ifx CC=mpiicx CFLAGS=-O3 FFLAGS=-O3 MPIF90=mpiifx  
--with-hdf5="/opt/hdf5" --enable-wannier90 && \

make all && \

rm ../qe-7.2.zip


Unfortunately, I get an error when I run it:

1117.3 mbdlib.f90(26): error #7002: Error in opening the compiled module file.  
Check INCLUDE paths.   [MBD]

1117.3   USE mbd,  ONLY : mbd_input_t, mbd_calc_t

1117.3 --^

1117.3 mbdlib.f90(40): error #6406: Conflicting attributes or multiple 
declaration of name.   [MBD_INPUT_T]

1117.3   TYPE(mbd_input_t):: inp

1117.3 ---^

1117.3 mbdlib.f90(41): error #6406: Conflicting attributes or multiple 
declaration of name.   [MBD_CALC_T]

1117.3   TYPE(mbd_calc_t):: calc

1117.3 ---^

1117.3 mbdlib.f90(26): error #6580: Name in only-list does not exist or is not 
accessible.   [MBD_INPUT_T]

1117.3   USE mbd,  ONLY : mbd_input_t, mbd_calc_t

1117.3 ---^

1117.3 mbdlib.f90(26): error #6580: Name in only-list does not exist or is not 
accessible.   [MBD_CALC_T]

1117.3   USE mbd,  ONLY : mbd_input_t, mbd_calc_t

1117.3 ^

1117.3 mbdlib.f90(63): error #6404: This name does not have a type, and must 
have an explicit type.   [INP]

1117.3   ALLOCATE(inp%atom_types(nat))

1117.3 ---^

1117.3 mbdlib.f90(82): error #6303: The assignment operation or the binary 
expression operation is invalid for the data types of the two operands.   [TRIM]

1117.3 inp%atom_types(na) = trim(atm(ityp(na)))

1117.3 -^

1117.3 mbdlib.f90(84): error #6366: The shapes of the array expressions do not 
conform.   [INP]

1117.3   inp%coords = tau*alat  ! HK-TODO: this one works for PW (check if it 
is for CP)

1117.3 --^

1117.3 mbdlib.f90(90): error #6366: The shapes of the array expressions do not 
conform.   [INP]

1117.3 inp%lattice_vectors = at*alat  ! Lattice vector in real space

1117.3 ^

1117.3 mbdlib.f90(94): error #6366: The shapes of the array expressions do not 
conform.   [INP]

1117.3   inp%k_grid = [nk1, nk2, nk3]

1117.3 --^

1117.3 mbdlib.f90(101): error #6366: The shapes of the array expressions do not 
conform.   [INP]

1117.3   inp%k_grid = [1, 1, 1] !set default k points grid

1117.3 --^

1117.3 mbdlib.f90(122): error #6404: This name does not have a type, and must 
have an explicit type.   [CALC]

1117.3   CALL calc%init(inp)

1117.3 ---^

1117.3 mbdlib.f90(184): error #6830: The argument of the ALLOCATED intrinsic 
cannot be a constant or an expression.   [INP]

1117.3   IF(ALLOCATED(inp%atom_types)) DEALLOCATE(inp%atom_types)

1117.3 ---^

1117.3 compilation aborted for mbdlib.f90 (code 1)

1117.3 make[1]: *** [../make.inc:16: mbdlib.o] Error 1

1117.3 make[1]: Leaving directory '/opt/q-e-qe-7.2/Modules'

1117.3 make: *** [Makefile:194: mods] Error 1

Could you please provide your thoughts, what could be the solution here?
Also, perhaps, you have already compiled QEs with the new compilers and know 
which options to use - if so, I'd appreciate that information!


Best,

Sergei


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Re: [QE-users] QE crashing right after "Starting wfcs"

[Pietro Davide Delugas]

Most likely the processes are killed because they try to allocate more memory 
per node than allowed in this SKU. This should reported on stderr.

Il 14 ago 2023 2:09 PM, Luis Cebamanos  ha scritto:
Hello,

I am trying to find out why QE crashes right after printing out the following:

 number of k points= 1
   cart. coord. in units 2pi/alat
k(1) = (   0.000   0.000   0.000), wk =   2.000

 Dense  grid: 27637241 G-vectors FFT dimensions: ( 540, 540, 540)

 Smooth grid:  9771712 G-vectors FFT dimensions: ( 375, 375, 375)

 Estimated max dynamical RAM per process >   4.42 GB

 Estimated total dynamical RAM >1125.78 GB

 Initial potential from superposition of free atoms

 starting charge5231.9496, renormalised to5232.

 negative rho (up, down):  6.436E-01 0.000E+00
 Starting wfcs are 5168 randomized atomic wfcs

===
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 13 PID 220321 RUNNING AT maryland
=   KILLED BY SIGNAL: 9 (Killed)
===

I cannot see anything in the logs and I can run well on a different SKU with 
less cores/node. How could I get a bit more info about this crash? Is there a 
way to find out what the problem could be?

Regards,

Chris


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Re: [QE-users] QE Intel: WARNING: release_mt library was used but no multi-ep feature was enabled. Please use release library instead.

[Pietro Davide Delugas]

Hello
The message probably comes from the intelmpi library.  You are using the 
multithreaded one but the program does not use these features.
If you link the non non-multithreaded releasen  the message should disappear.
I don't know if the intelmpi multithreaded works fine,  or if there is any 
performance loss  in using it.
Best regards
Pietro


Il 31 lug 2023 3:32 PM, Anton Lopis  ha scritto:



Hi All,

I support our users of CHPC SA in Materials Science and Chemistry.
We are seeing this warning in our output for somje of our Intel compiled 
versions of QE.

WARNING: release_mt library was used but no multi-ep feature was enabled. 
Please use release library instead.

I have tried to google this, but info is not that helpful.

Jobs appear to run ok, but we are not fully sure whether the results might 
differ or the speed and parallelisation might be affected.

Please advise on whether this warning is significant or can be ignored.

Much appreciated,
Anton


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[QE-users] R: Assistance with the Installation of Quantum Espresso

[Pietro Davide Delugas]

Hello
Could you explain better what is the issue ?
Just provide error messages logs etc.
 Pietro

Da: users  per conto di MOSES NTSIFUL 

Inviato: lunedì 10 luglio 2023 12:14
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Assistance with the Installation of Quantum Espresso

Dear Developers,
I have tried the suggestion(steps) for the installation of the Quantum Espresso 
for Ubuntu  20.04 (Description: Ubuntu 20.04.5 LTS) but it still didn't work 
out.

 I would really appreciate further suggestions. Thank you.

Best regards,
Moses Ntsiful.
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[QE-users] R: Question on local atomic charge

[Pietro Davide Delugas]

Hello

The local magnetic moments are used in the program for the implementation of 
the magnetic constraints. So they are defined to avoid overlaps and maximize 
coverage. Their usage for the constraints needs some caution. Still, it's 
quicker than other methods and easier to implement.

For what concerns the information, I agree that it is mostly qualitative. I 
think it may be helpful for quick inspection and recognition of the ground 
state magnetic pattern you have obtained. More rigorous evaluation of local 
magnetic moments, which are unfeasible during the SCF calculation, can be done 
during post-processing.
Pietro

Da: users  per conto di Mpayami via 
users 
Inviato: venerdì 7 luglio 2023 01:45
A: Quantum ESPRESSO users Forum 
Oggetto: Re: [QE-users] Question on local atomic charge

With a small modification in the formula, I got better results that was 
consistent with what I was looking for.
However, I am now convinced that the information in its present form is quite 
useful.

Mahmoud


- Original Message -

From: Mpayami (mpay...@aeoi.org.ir)
Date: 14/04/1402 06:27
To: Mpayami (mpay...@aeoi.org.ir), Quantum ESPRESSO 
users Forum 
(users@lists.quantum-espresso.org)
Subject: Re: [QE-users] Question on local atomic charge

In the routine "make_makepointlists.f90" it is explained how "r_m" (i.e. R0 in 
my post) is determined automatically.
Is it possible to change it to say vd_Waals radius for an atom?

Bests,
Mahmoud


- Original Message -

From: Mpayami via users 
(users@lists.quantum-espresso.org)
Date: 13/04/1402 22:22
To: Quantum ESPRESSO users Forum 
(users@lists.quantum-espresso.org)
Subject: [QE-users] Question on local atomic charge

Hi All.

I noticed that the calculated electronic charges on atoms which is done by 
CALLing "get_locals.f90" in "report_mag.f90" in an SCF cycle are somewhat 
different from
the values obtained when running "projwfc".
The origin of this difference maybe in taking (?) different "atomic radius", 
R0, in the two methods over which the charge integration is done; or
using low-density k-mesh and lower values of "nbnd" in SCF calculation.
If the latter is true, then how can one benefit the information provided by 
"report_mag.f90" ?
Any comments is highly appreciated.

Best regards,

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


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[QE-users] R: Assistance with the Installation of Quantum Espresso on Ubuntu

[Pietro Davide Delugas]

Dear Moses

On Ubuntu, things should be easy.

You need to install a few necessary packages with apt.

sudo apt install gfortran libopenmpi-dev libopenblas-dev git autoconf

Then download the latest release from 
https://www.quantum-espresso.org/download-page/

Expand the archive that you have downloaded:

tar xzf qe-7.2-ReleasePack.tar.gz

Then just go into the q-e directory that has been created, and run the 
configure command:

./configure

And then compile everything with

make all

If everything works the executable will be in the  /bin directory ready to use.

I hope this helps, best regards
Pietro









Da: users  per conto di MOSES NTSIFUL 

Inviato: martedì 4 luglio 2023 21:58
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Assistance with the Installation of Quantum Espresso on 
Ubuntu

Dear Quantum Espresso Support Team,

I hope this email finds you well. I am a graduate student of the
University of Cape Coast - Ghana, offering a Master of
Philosophy(Physics). I am writing to seek assistance with the
installation of Quantum Espresso on Ubuntu. I have encountered some
difficulties during the installation process and would sincerely
appreciate your guidance and support.

I am using Ubuntu  20.04 (Description: Ubuntu 20.04.5 LTS) and have
attempted to install Quantum Espresso following the provided
installation instructions from different tutorials on YouTube but have
never been successful.

Specifically, I would appreciate any step-by-step instructions or
recommendations to ensure a successful installation on my Ubuntu with
any suitable Quantum Espresso version as it would be suggested by the
Quantum Espresso Support Team.

 I look forward to your guidance and instructions to successfully
install Quantum Espresso on my Ubuntu system. Thank you.


Best regards,
Moses Ntsiful.
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[QE-users] R: Data Parallelism and GPU Support for Quantum Espresso

[Pietro Davide Delugas]

Dear Prashant

For what concerns GPU, the branch you are referring to is outdated.
More recent releases of QE are available on the download page
https://www.quantum-espresso.org/download-page/
and they can all be compiled for CUDA GPUs

About the parallel execution: in QE, there is the manypw.x application that can 
run many inputs in parallel.

But for such a large number of systems, also considering that you'll be running 
a workflow for each of them, it is
much better to use a workflow manager, for example, AiiDA
https://www.aiida.net/sections/about.html

Best regards and greetings
Pietro

Da: users  per conto di Prashant 
Govindarajan via users 
Inviato: giovedì 29 giugno 2023 22:49
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Data Parallelism and GPU Support for Quantum Espresso

Greetings,

I have been using Quantum Espresso for performing SCF calculations to compute 
the band gap and energies of crystal structures. Is there a way to perform DFT 
simulations on a large number of input crystals parallely using QE, i.e., data 
parallelism across multiple inputs (in addition to parallel calculations for 
each crystal)? For instance, what is the most optimal way to run the pw.x 
command for say 5000+ crystals?

Further, I am aware that there is GPU support for QE. There are issues while 
trying to install GPU-enabled QE which I am trying to figure out, but I was 
wondering if it provides reasonable speedup especially when I am dealing with 
multiple crystals. Also, I've been referring to https://gitlab.com/QEF/q-e-gpu 
for GPU-enabled QE installation. If there are any other useful resources please 
let me know.

I am using QE as an evaluation scheme for deep learning outputs, so an 
effective way for GPU-based DFT simulation would be of great help.

Thanks and Regards

Prashant Govindarajan
1st year PhD Student
Mila-Quebec AI Institute
Montreal, QC


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[QE-users] R: R: [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched directive

[Pietro Davide Delugas]

The  "__GPU_MPI" flag is not strictly necessary to compile and run the MPI 
parallel versions with GPU.
It only enables more efficient communications when the MPI library has been 
compiled with the necessary support for GPU-aware communications. The only 
essential flag for MPI is the  -D__MPI.
The failure's origin might be that your MPI library lacks such support. But you 
had better ask your system administrator about this.

You can remove the GPU_MPI flag and see if the code works.

Hope it helps
Pietro

Da: users  per conto di Siwakorn 
Sukharom 
Inviato: giovedì 25 maggio 2023 06:34
A: Paolo Giannozzi ; Quantum ESPRESSO users Forum 

Oggetto: Re: [QE-users] R: [QE-GPU] compilation issue : 
NVFORTRAN-F-1225-Unmatched directive


Now, I can compiled GPU version for QE 7.2. Thank you for the suggestion. It 
can run fine on 1 gpu. However, I still having a problem with running multiple 
gpus. I have added the --with-cuda-mpi=yes during the configuration, and I can 
see that there is -D__GPU_MPI tag on DFLAGS in make.inc


When compiled and run on multiple gpus, I get the error message below:


%%
 Error in routine  fft_buffers (4):
  Allocation failed
 %%

 stopping ...
MPICH ERROR [Rank 0] [job id 77558.0] [Thu May 25 11:11:15 2023] 
[x1000c2s0b0n1] - Abort(4) (rank 0 in comm 0): application called 
MPI_Abort(MPI_COMM_WORLD, 4) - process 0

aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 4) - process 0

What is happening?


From: Paolo Giannozzi 
Sent: Wednesday, May 24, 2023 1:05:38 PM
To: Siwakorn Sukharom; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] R: [QE-GPU] compilation issue : 
NVFORTRAN-F-1225-Unmatched directive

On 24/05/2023 05:47, Siwakorn Sukharom wrote:
>
> I have added -D__OPENACC to DFLAGS for QE 7.2 and 7.1

"-D_OPENACC", with one underscore

Paolo

. The compilation
> was failed for QE 7.2, but success for QE 7.1. The 
> https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fmake.inc&c=E,1,RCjygUVrHz_y_vPiylqafXnFbjj3qIZgqer4PcMPTMAL1nWOb0F2WH7i2o4bEwXkmPY9pBKdip8024dPJMlrqTn00xrWzoEusar_ykVw&typo=1
>  is almost
> the same.
>
> 
> *From:* Paolo Giannozzi 
> *Sent:* Tuesday, May 23, 2023 5:29:09 PM
> *To:* Quantum ESPRESSO users Forum; Siwakorn Sukharom
> *Subject:* Re: [QE-users] R: [QE-GPU] compilation issue :
> NVFORTRAN-F-1225-Unmatched directive
> On 5/23/23 12:13, Siwakorn Sukharom wrote:
>
>> I can successfully compile on QE version 7.1, but not 7.2. The error
>> is still the same. Will focus on 7.1 instead.
>
> Not a good idea. You just need to add _OPENACC to DFLAGS (something that
> the Cray compiler should take care of, but it doesn't).
>
> Paolo
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
>
> 
>
> Disclaimer:
>
> This e-mail and any files transmitted with it may contain confidential
> and proprietary information of the National Science and Technology
> Development Agency (NSTDA), Thailand. They are intended solely for the
> use of the addressed individuals or entities. If you are not the
> intended recipient, you are required to immediately delete this e-mail
> and its contents from your system. Any disclosure, distribution, or
> action based upon the contents of this e-mail is strictly prohibited.
> Any views or opinions presented in this e-mail are solely those of the
> sender and do not necessarily represent those of NSTDA. NSTDA does not
> accept any responsibility for the content of this message or the
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216



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[QE-users] R: [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched directive

[Pietro Davide Delugas]

As the compiler is compiling a _tmp file, you are most likely using cpp or some 
external preprocessor.
You should check that the preprocessing is done by the nvfortran compiler with 
the -acc option passed.


Otherwise,  you can try adding by hand the -D_OPENACC to the DFLAGS on 
MANUAL_DFLAGS variables in the "make.inc"  file

hope it helps
Pietro

Da: users  per conto di Siwakorn 
Sukharom 
Inviato: martedì 23 maggio 2023 06:47
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched 
directive


I try to compile QE for gpu. My HPC system is AMD EPYC™ 7713 + Nvidia A100, and 
it is based on Cray programming environment. For compilation, i used nvhpc/22.7 
+ cray-mpich + cray-fftw


For configure i use this and edit in make.inc later

./configure --enable-parallel --with-scalapack=no \
CC=cc CXX=CC FC=ftn F77=ftn F90=ftn MPICC=cc MPICXX=CC MPIF77=ftn MPIF90=ftn \
FFT_LIBS="-L$FFTW_ROOT/lib -lfftw3" \
--with-cuda=/opt/nvidia/hpc_sdk/Linux_x86_64/22.7/cuda --with-cuda-cc=80 
--with-cuda-runtime=11.7 --enable-openmp \


Here is my make.inc

https://drive.google.com/file/d/1HfVtuRXsburug_Ks6wcsSDwrA6m0QHaH/view?usp=sharing


The error when I compiled is


ftn -O1   -D__FFTW3 -D__CUDA -D__MPI  -cuda -gpu=cc80,cuda11.7 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//external/devxlib/src
 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//external/devxlib/include
 -acc 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//external/devxlib/src
 -I. -I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//include 
-I/opt/cray/pe/fftw/3.3.10.3/x86_milan/include 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//upflib 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//XClib 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//Modules 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//FFTXlib/src 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//LAXlib 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//UtilXlib 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//MBD 
-I/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu//KS_Solvers  
-I../../dft-d3/ -c drhoc_tmp.f90 -o drhoc.o
NVFORTRAN-F-1225-Unmatched directive END - DATA. (drhoc_tmp.f90: 90)
NVFORTRAN/x86-64 Linux 22.7-0: compilation aborted
make[2]: *** [../../make.inc:16: drhoc.o] Error 2
make[2]: *** Waiting for unfinished jobs

any suggestion?






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[QE-users] R: Convert pseudo from fhi to upf format

[Pietro Davide Delugas]

Hello
There is now a single program called upfconv.f90 inside the upflib directory. 
It should work for all old formats.
If you have compiled pw or one of the other main tags of the Makefile, you 
should find the executable in the upflib directory. Otherwise, you can compile 
it directly with

make libupf

Best regards
Pietro

Da: users  per conto di Jibiao Li via 
users 
Inviato: mercoledì 10 maggio 2023 05:26
A: users 
Oggetto: [QE-users] Convert pseudo from fhi to upf format


Dear ALL,

I want to convert pseudo from fhi to upf format. I searched the mailist and it 
suggested that fhi2upf.x serves the purpose. However, I can not even find 
upftools in the recent release of QE. How can I compile the code to generate 
fhi2upf.x? Any other method to convert pseudo from fhi to upf format?

Can anyone show me the answer?


Thank you very much!


Regards



Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 
54944118000

Web of Science Research ID: 
http://www.webofscience.com/wos/author/record/GLS-7259-2022




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Re: [QE-users] "q-mesh breaks symmetry" problème.

[Pietro Davide Delugas]

Hello
I guess the reason for your issue is that for some lattice constants  your fft 
mesh is incompatible with the symmetry operations within the phonon code. In 
other cases no. Try to set use_all_frac to false.
Pietro


Il 8 mag 2023 12:22 PM, Pierre Linères via users 
 ha scritto:
Bonjour,

Je suis étudiant en master 2 de géologie et dans le cadre de mon stage de 
recherche de fin d'étude j'étude les transitions de certaines phases via des 
méthodes de calculs ab-initio. Actuellement je m'intéresse à la Reidite 
(ZrSiO4-tétragonal). Plus particulièrement, je suis en train d'effectuer des 
calculs de fréquences phononiques en calculant des matrices dynamiques et de 
constantes de forces pour plusieurs pressions (0 à 300 kbar avec un step de 
20kbar). Cependant, je rencontre le problème suivant :

Pour les pressions ;  60kbar / 80kbar / 160kbar / 180kbar / 220kbar / 240kbar / 
280kbar / 300kbar, l'erreur suivante "q-mesh breaks symmetry" s'affiche dans 
mes fichiers *ph.out et le calcul s'arrête (voir la première image).

Pour les autres pressions tout fonctionne très bien ...

Nous avons exploré plusieurs pistes mais sans succès (toujours la même erreur) :

- Utilisation de différentes versions de q.e (6.2 / 6.6 / 5.1.1 / 6.4.1 ).
- Utilisation de plusieurs grilles de q-points (333 / 332 / 444 / 442 / 555 / 
552).
- Utiliser ibrav = 7 en reconstituant celldm(1) et celldm(3)  au lieu de ibrav 
=0.

L'incompréhension réside principalement dans le fait que les calculs 
fonctionnent très bien pour certaines pressions et pas pour certaines.
Je mets dans le mail mon script "job.reidite-60kbarT_ib7" (celui qui calcule à 
P=60kbar), il contient à la fois les informations pour ibrav = 0 et ibrav = 7.

Je m'excuse d'avance si certains points ne sont pas clairs (c'est la première 
fois que je publie et que je travaille dans ce domaine). Je reste entièrement à 
disposition si vous avez la moindre question.

Je vous remercie de l'attention que vous porterez à mon problème.

Cordialement,

Pierre.


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[QE-users] R: Fwd: error in routine check atoms(1)

[Pietro Davide Delugas]

Hello

I haven't checked, but it looks like a simple cubic cell.  Try replacing 
ibrav=2 with ibrav=1
Pietro

Da: users  per conto di 
SPPU/05097P/2021 OYOMO BILL C 
Inviato: mercoledì 12 aprile 2023 06:48
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Fwd: error in routine check atoms(1)



-- Forwarded message -
From: SPPU/05097P/2021 OYOMO BILL C 
mailto:billclinton...@students.tukenya.ac.ke>>
Date: Sun, Apr 9, 2023 at 8:37 PM
Subject: error in routine check atoms(1)
To: 
mailto:users-requ...@lists.quantum-espresso.org>>


Hello everyone,
I get the following error I try to run an MD calculation using a supercell 
created by xcrysden:
%%
 Error in routine check_atoms (1):
 atoms #   1 and #  25 differ by lattice vector ( 0,-1, 0) in crystal axis
 %%

 stopping ...
How do I solve the problem? Kindly look at the attached input file. Also, 
please let me know If there is any other tool for generating a supercell with 
atoms of the same unit cell arranged together rather than atoms of the same 
type of elements arranged together, which is what phonopy generates.
Thank you,
Bill C Oyomo.
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[QE-users] R: Hydrogen atom pseudopotential files with q=1.25e and q=0.75e (PBE, USPP)

[Pietro Davide Delugas]

Hello
You may find them close to the bottom of this page.
http://pseudopotentials.quantum-espresso.org/legacy_tables/original-qe-pp-library/h

They are for  LDA, but given that you are using them for the artificial 
passivation of dangling bonds, hopefully, the actual objective of your 
calculation is far enough from those bonds, and they may also do fine with 
other functionals provided that you specify the functional in input using the 
input_dft input variable.
I hope it helps; best regards
Pietro

Da: users  per conto di GOKHAN HASEKI 

Inviato: lunedì 10 aprile 2023 21:02
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Hydrogen atom pseudopotential files with q=1.25e and 
q=0.75e (PBE, USPP)

Hi

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=1.25e 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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[QE-users] R: Query regarding error in latest QE version 7.0

[Pietro Davide Delugas]

Hello

there are 2 typos &CONTOL instead of &CONTROL and la2F=.ture. instead of 
la2F=.true.,
fixed these, the input works with the latest version of QE 7.1 and with the 
very close next-to-come 7.2
I hope this helps
kind regards
Pietro


Da: users  per conto di zhouchao via 
users 
Inviato: giovedì 23 marzo 2023 08:51
A: users 
Oggetto: [QE-users] Query regarding error in latest QE version 7.0


Dear QE expert,

I hope this email finds you well. I am writing to seek your assistance on an 
issue I encountered when using the latest version of Quantum Espresso (QE) 
v7.0. When I input the PW file for my simulation, the program encountered an 
error and crashed. Surprisingly, when I tried to use the compiled version of QE 
v6.4, the same PW file was running smoothly without any issues.

I am confused about the cause of this error and wanted to know if there are any 
compatibility issues between the two versions of QE? Moreover, the crash file 
is nothing, which made it difficult for me to detect and diagnose the error.

I would appreciate it if you could share your insights and guide me on the 
right path to identify and solve this error. Please let me know if you require 
any further information from my side.

Thank you for your time and attention.

Best regards,

zhouchao


the input is as follow

&CONTOL

calculation='scf', disk_io='low', prefix='MoB',

pseudo_dir='./', outdir='./tmp', verbosity='high'

tprnfor=.true., tstress=.true., forc_conv_thr=1.0d-5

/

&SYSTEM

ibrav= 0,

celldm(1) = 1.8897261328856432, ! a.u. to Angst

nat= 3, ntyp= 2,

occupations = 'smearing', smearing = 'gauss', degauss = 0.03

ecutwfc= 80, ecutrho = 400,

la2F=.ture.

/

&ELECTRONS

conv_thr = 1.0d-9

mixing_beta = 0.8d0

diagonalization = 'david'

/

ATOMIC_SPECIES

  Mo 95.94  Mo.UPF

  B  10.81 B.UPF

CELL_PARAMETERS (alat=  1.88972613)

  2.948407025   0.0  -0.0

  -1.474203513   2.553395385  -0.0

   0.0   0.0   3.221035860

ATOMIC_POSITIONS (crystal)

Mo   0.0  -0.0   0.0

B0.33343   0.66687   0.5

B0.66627   0.33313   0.5

K_POINTS {automatic}

  21 21  15 0 0 0




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[QE-users] R: R: unconverged issue in spin-polarized SCAN calculations

[Pietro Davide Delugas]

Hello

Sorry for the previous message in Italian.

One of the issues could be that the pseudos have been generated with PBE and 
then used with the SCAN functional, this can in some cases create issues as the 
one you have reported. Could you provide more information about the pseudo that 
you have used?
thanks and regards
Pietro

Da: users  per conto di Pietro Davide 
Delugas 
Inviato: mercoledì 15 marzo 2023 09:38
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] R: unconverged issue in spin-polarized SCAN calculations

ok
gli chiediamo gli pseudi, per il resto abbiamo tutto.
sembrerebbe un problema collegato allo scan, alle volte se si usano pseudi PBE 
i sistemi tendono a esplodere.

Da: users  per conto di Giuseppe 
Mattioli 
Inviato: martedì 14 marzo 2023 12:35
A: users@lists.quantum-espresso.org 
Oggetto: Re: [QE-users] unconverged issue in spin-polarized SCAN calculations


Dear Yi-min Ding
Supposing that the pristine silicon nitride cell converges without
problems, try first to use smearing (uncomment the lines) and to
reduce mixing_beta to a low or very low value (0.1-0.01). I don't know
silicon nitride very well, so excuse me for the possibly stupid
question. Have you tried to use a larger supercell? 33% Al doping
might be not only unphysical, but also the source of wild instability
in scf iterations.
HTH
Giuseppe

Quoting 丁以民 via users :

> Dear all,
> I am doing a scf calculation for a FM system using SCAN functional.
> But, the energy in output file is positive, and the run shown no
> converged tendency.
>
>
> The input and out files are shown below:.
> input:
> &system
>    ibrav =4
>    a=2.9063917063813576
>    c=25
>    nat = 7
>    ntyp = 3
>    ecutwfc = 100.0
>    nbnd=48
>    nspin=2
>    ! starting_magnetization(1)= 0,
>    ! starting_magnetization(2)=0,
>    ! starting_magnetization(3)=1,
>      tot_magnetization =1
>    ! occupations='smearing',
>    ! smearing='gauss',
>    ! degauss=1.0d-2,
>     input_dft='scan'
> /
> &electrons
>    electron_maxstep = 100
>    conv_thr = 1.0d-8
>    mixing_mode = 'plain'
>    mixing_beta = 0.7
>    mixing_ndim = 8
>    diagonalization = 'david'
>    diago_david_ndim = 4
>    diago_full_acc = .true.
> /
> ATOMIC_SPECIES
>    Al  26.98  Al.upf
>    Si  28.09   Si.upf
>    N   14.01   N.upf
> ATOMIC_POSITIONS (crystal)
> Al 0.6643  0.3357 
> 0.5000   
> Si  0.  0.  0.3860058177698406
> Si  0.33342996  0.66687029 
> 0.6139941822301592 
> N  0.  0. 
> 0.4563348732468989 
> N  0.33342996  0.66687029 
> 0.5436651267531011 
> N  0.33342996  0.66687029 
> 0.3651769401128088 
> N 0. -0.  0.6348230598871913 
> K_POINTS automatic
>  11 11 1 0 0 0
>
> .
> output:
>      ...
>      iteration # 99     ecut= 
>  100.00 Ry     beta= 0.70
>      Davidson diagonalization with overlap
>      c_bands:  3 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      ethr =  1.00E-02,  avg # of iterations = 24.8
>
>
>      negative rho (up,down):  5.052E+00 2.651E+00
>
>
>      total cpu time spent up to now is   
>  1964.0 secs
>
>
>      total energy         
>     =    3309.58902363 Ry
>      estimated scf accuracy    < 
> 304153.85545920 Ry
>
>
>      total magnetization     
>  =     1.00 Bohr mag/cell
>      absolute magnetization    = 
>   28.84 Bohr mag/cell
>
>
>      iteration #100     ecut= 
>  100.00 Ry     beta= 0.70
>      Davidson diagonalization with overlap
>      ethr =  1.00E-02,  avg # of iterations = 12.3
>
>
>      negative rho (up,down):  3.516E+00 2.027E+00
>
>
>      total cpu time spent up to now is   
>  1974.9 secs
>
>
>      total energy         
>     =    2760.95716210 Ry
>      estimated scf accuracy    < 
> 488812.03105752 Ry
>
>
>      total magnetization     
>  =     1.00 Bohr mag/cell
>      absolute magnetization    = 
>   30.68 Bohr mag/cell
>
>
>      End of self-consistent calculation
>
>
>      convergence NOT achieved after 100 iterations: stopping
>      Writing meta-gga kinetic term
>
> .

[QE-users] R: unconverged issue in spin-polarized SCAN calculations

[Pietro Davide Delugas]

ok
gli chiediamo gli pseudi, per il resto abbiamo tutto.
sembrerebbe un problema collegato allo scan, alle volte se si usano pseudi PBE 
i sistemi tendono a esplodere.

Da: users  per conto di Giuseppe 
Mattioli 
Inviato: martedì 14 marzo 2023 12:35
A: users@lists.quantum-espresso.org 
Oggetto: Re: [QE-users] unconverged issue in spin-polarized SCAN calculations


Dear Yi-min Ding
Supposing that the pristine silicon nitride cell converges without
problems, try first to use smearing (uncomment the lines) and to
reduce mixing_beta to a low or very low value (0.1-0.01). I don't know
silicon nitride very well, so excuse me for the possibly stupid
question. Have you tried to use a larger supercell? 33% Al doping
might be not only unphysical, but also the source of wild instability
in scf iterations.
HTH
Giuseppe

Quoting 丁以民 via users :

> Dear all,
> I am doing a scf calculation for a FM system using SCAN functional.
> But, the energy in output file is positive, and the run shown no
> converged tendency.
>
>
> The input and out files are shown below:.
> input:
> &system
>    ibrav =4
>    a=2.9063917063813576
>    c=25
>    nat = 7
>    ntyp = 3
>    ecutwfc = 100.0
>    nbnd=48
>    nspin=2
>    ! starting_magnetization(1)= 0,
>    ! starting_magnetization(2)=0,
>    ! starting_magnetization(3)=1,
>      tot_magnetization =1
>    ! occupations='smearing',
>    ! smearing='gauss',
>    ! degauss=1.0d-2,
>     input_dft='scan'
> /
> &electrons
>    electron_maxstep = 100
>    conv_thr = 1.0d-8
>    mixing_mode = 'plain'
>    mixing_beta = 0.7
>    mixing_ndim = 8
>    diagonalization = 'david'
>    diago_david_ndim = 4
>    diago_full_acc = .true.
> /
> ATOMIC_SPECIES
>    Al  26.98  Al.upf
>    Si  28.09   Si.upf
>    N   14.01   N.upf
> ATOMIC_POSITIONS (crystal)
> Al 0.6643  0.3357 
> 0.5000   
> Si  0.  0.  0.3860058177698406
> Si  0.33342996  0.66687029 
> 0.6139941822301592 
> N  0.  0. 
> 0.4563348732468989 
> N  0.33342996  0.66687029 
> 0.5436651267531011 
> N  0.33342996  0.66687029 
> 0.3651769401128088 
> N 0. -0.  0.6348230598871913 
> K_POINTS automatic
>  11 11 1 0 0 0
>
> .
> output:
>      ...
>      iteration # 99     ecut= 
>  100.00 Ry     beta= 0.70
>      Davidson diagonalization with overlap
>      c_bands:  3 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      c_bands:  5 eigenvalues not converged
>      ethr =  1.00E-02,  avg # of iterations = 24.8
>
>
>      negative rho (up,down):  5.052E+00 2.651E+00
>
>
>      total cpu time spent up to now is   
>  1964.0 secs
>
>
>      total energy         
>     =    3309.58902363 Ry
>      estimated scf accuracy    < 
> 304153.85545920 Ry
>
>
>      total magnetization     
>  =     1.00 Bohr mag/cell
>      absolute magnetization    = 
>   28.84 Bohr mag/cell
>
>
>      iteration #100     ecut= 
>  100.00 Ry     beta= 0.70
>      Davidson diagonalization with overlap
>      ethr =  1.00E-02,  avg # of iterations = 12.3
>
>
>      negative rho (up,down):  3.516E+00 2.027E+00
>
>
>      total cpu time spent up to now is   
>  1974.9 secs
>
>
>      total energy         
>     =    2760.95716210 Ry
>      estimated scf accuracy    < 
> 488812.03105752 Ry
>
>
>      total magnetization     
>  =     1.00 Bohr mag/cell
>      absolute magnetization    = 
>   30.68 Bohr mag/cell
>
>
>      End of self-consistent calculation
>
>
>      convergence NOT achieved after 100 iterations: stopping
>      Writing meta-gga kinetic term
>
> ...
> Can you give me some help?
> Thanks in advance.
> Dr. Yi-min Ding



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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peo

Re: [QE-users] FoX: xml_AddCharacters Error

[Pietro Davide Delugas]

Hello
It's most likely a bug, hopefully one of those that were fixed in the newer 
versions.
Regards - Pietro

Il 6 feb 2023 9:20 AM, "Mr. Sheharyar Pervez RA FES"  ha 
scritto:
When running an scf calculation on QE 6.4.1, I get the following from FoX:
ERROR(FoX)
xml_AddCharacters: Invalid character in chars

The calculation runs fine but no xml file is generated.  the following files 
are created:

.
├── kgec.in
├── qmof-f2ae0a5.save
│   ├── charge-density.dat
│   ├── data-file-schema.xml
│   └── paw.txt
├── qmof-f2ae0a5_scf.in
├── qmof-f2ae0a5_scf.out
└── qmof-f2ae0a5.wfc1

I'm not sure where this invalid character comes from because the entire input 
file is in standard ascii format. How to go about solving this?
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[QE-users] R: Quantume Espresso 6.1, 6.4.1, 6.5

[Pietro Davide Delugas]

Dear Krishendu,
I would expect so.
There may be very few cases where bugs or regressions affect the results. You 
can have a look at the
Doc/release-notes file to check if the changes and issues for the versions you 
are interested in involve your calculations.

Pietro



Da: users  per conto di KRISHNENDU 
MUKHERJEE 
Inviato: giovedì 26 gennaio 2023 12:26
A: users 
Oggetto: [QE-users] Quantume Espresso 6.1, 6.4.1, 6.5


Dear Community,

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


Regards,
Krishnendu


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[QE-users] R: R: R: Reading displacements from the matdyn.modes file

[Pietro Davide Delugas]

You must preserve the proportion --and, if the displacements are complex,  the 
phase differences- among the mode components.

Your procedure doesn't do that unless you write the displaced geometry in 
fractional coordinates and your system is orthorhombic.

It's much simpler to use alat coordinates so that you can add the scaled 
displacement as it is.
Pietro



Da: users  per conto di Piotr 
Szkudlarek 
Inviato: mercoledì 25 gennaio 2023 14:54
A: Quantum ESPRESSO users Forum 
Oggetto: Re: [QE-users] R: R: Reading displacements from the matdyn.modes file

Dear Pietro,
to create the displaced geometries, I added the 1st, 3rd and 5th number in the 
matrix divided by x, y and z cell sizes and then multiplied by an arbitral 
scaling factor (in my case - 0.1)). Is that a proper way to create the 
displaced geometry?
Yours sincerely.,
Piotr Szkudlarek

śr., 25 sty 2023 o 14:48 Pietro Davide Delugas 
mailto:pdelu...@sissa.it>> napisał(a):
Dear Piotr
It is just a normalized 3Xnat vector  --normalized such that the sum of the 
squared moduli of all displacements yields one. They give you the relative 
amplitudes and phases of the atomic displacements in that mode.  The net 
amplitude would depend on the energy stored in that mode and its reduced mass.

Hope it helps
Pietro

Da: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 per conto di Piotr Szkudlarek 
mailto:p.szkudla...@cent.uw.edu.pl>>
Inviato: mercoledì 25 gennaio 2023 13:22
A: Quantum ESPRESSO users Forum 
mailto:users@lists.quantum-espresso.org>>
Oggetto: Re: [QE-users] R: Reading displacements from the matdyn.modes file

Dear Pietro,
Thank you very much for your answer. I have another question: are those numbers 
in Angstrom or what units?
Regards,
Piotr Szkudlarek


pon., 23 sty 2023 o 11:28 Pietro Davide Delugas 
mailto:pdelu...@sissa.it>> napisał(a):
Hello Piotr
The displacements' components are complex numbers; thus, six floats.

Pietro

Da: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 per conto di Piotr Szkudlarek 
mailto:p.szkudla...@cent.uw.edu.pl>>
Inviato: lunedì 23 gennaio 2023 10:55
A: Quantum ESPRESSO users Forum 
mailto:users@lists.quantum-espresso.org>>
Oggetto: [QE-users] Reading displacements from the matdyn.modes file

Dear QE community,
I would like to ask what is the meaning of 6 floats in matdyn.modes file. I can 
imagine that 3 of them show the coordinates of the displacements, but what are 
the other three? Also, which of them are the ones telling about the coordinates 
of the displacement?
Best,
Piotr Szkudlarek,
University of Warsaw
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[QE-users] R: R: Reading displacements from the matdyn.modes file

[Pietro Davide Delugas]

Dear Piotr
It is just a normalized 3Xnat vector  --normalized such that the sum of the 
squared moduli of all displacements yields one. They give you the relative 
amplitudes and phases of the atomic displacements in that mode.  The net 
amplitude would depend on the energy stored in that mode and its reduced mass.

Hope it helps
Pietro

Da: users  per conto di Piotr 
Szkudlarek 
Inviato: mercoledì 25 gennaio 2023 13:22
A: Quantum ESPRESSO users Forum 
Oggetto: Re: [QE-users] R: Reading displacements from the matdyn.modes file

Dear Pietro,
Thank you very much for your answer. I have another question: are those numbers 
in Angstrom or what units?
Regards,
Piotr Szkudlarek


pon., 23 sty 2023 o 11:28 Pietro Davide Delugas 
mailto:pdelu...@sissa.it>> napisał(a):
Hello Piotr
The displacements' components are complex numbers; thus, six floats.

Pietro

Da: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 per conto di Piotr Szkudlarek 
mailto:p.szkudla...@cent.uw.edu.pl>>
Inviato: lunedì 23 gennaio 2023 10:55
A: Quantum ESPRESSO users Forum 
mailto:users@lists.quantum-espresso.org>>
Oggetto: [QE-users] Reading displacements from the matdyn.modes file

Dear QE community,
I would like to ask what is the meaning of 6 floats in matdyn.modes file. I can 
imagine that 3 of them show the coordinates of the displacements, but what are 
the other three? Also, which of them are the ones telling about the coordinates 
of the displacement?
Best,
Piotr Szkudlarek,
University of Warsaw
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[QE-users] R: Reading displacements from the matdyn.modes file

[Pietro Davide Delugas]

Hello Piotr
The displacements' components are complex numbers; thus, six floats.

Pietro

Da: users  per conto di Piotr 
Szkudlarek 
Inviato: lunedì 23 gennaio 2023 10:55
A: Quantum ESPRESSO users Forum 
Oggetto: [QE-users] Reading displacements from the matdyn.modes file

Dear QE community,
I would like to ask what is the meaning of 6 floats in matdyn.modes file. I can 
imagine that 3 of them show the coordinates of the displacements, but what are 
the other three? Also, which of them are the ones telling about the coordinates 
of the displacement?
Best,
Piotr Szkudlarek,
University of Warsaw
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Re: [QE-users] Applying assume_isolated="2D" to modified anatase surface

[Pietro Davide Delugas]

Hello
These are your axes
  0.000   3.000   0.000
  1.000  -0.000  -2.539341738883929
  8.551   0.000   0.000

And this is the complaint of the code

2D CODE WILL NOT WORK, 2D MATERIAL NOT IN X-Y PLANE!!

Your surface is in the ZY plane. You need to reorient your system so that the 
surface stays in the XY plane.
You might still have problems, though, because the out of plane lattice vector 
is not orthogonal to the surface.
Pietro


From: users  On Behalf Of Léon 
Luntadila Lufungula
Sent: Thursday, December 1, 2022 12:13 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Applying assume_isolated="2D" to modified anatase surface

Dear QE users,

I recently learned that you have to apply a dipole correction when adsorbing 
molecules onto a surface when working under PBC. I know you can do this 
manually via the dipfield option, but the assume_isolated=”2D” option should 
have the same effect with the added benefit of truncating the Coulomb 
interaction in the z-direction. I have tried to re-do one of my calculations 
with this option enabled but I get the following error:

2D CODE WILL NOT WORK, 2D MATERIAL NOT IN X-Y PLANE!!

%%
 Error in routine vloc_of_g (1):
 2D cutoff is smaller than pseudo cutoff radius:  increase interlayer 
distance (or see Modules/read_pseudo.f90)
%%

Can somebody tell me how I can get this to work in my system? I don’t see how 
my material is not in the X-Y plane when looking at my structure. Could it be a 
problem because my cell is not orthogonal?

I don’t know if attachments work, so I’ll add my input description here (I only 
added the assume_isolated=”2D” flag compared to the original calculation):

&CONTROL
  calculation = 'relax'
  restart_mode = 'from_scratch'
  prefix = 'a101-3mppa-md1-2d'
  pseudo_dir = 
'/data/antwerpen/206/vsc20615/temp/quantumespresso/PSEUDOPOTENTIALS'
  outdir = '/scratch/antwerpen/206/vsc20615/quantumespresso/a101-3mppa-md1-2d'
  nstep = 200
  verbosity = 'high'
/
&SYSTEM
  ibrav = 0
  A =3.77449
  nat = 125
  ntyp = 6
  ecutwfc = 60
  ecutrho = 600
  spline_ps = .true.
  vdw_corr = "grimme-d2"
  assume_isolated = "2D"
!  nr1 = 180
!  nr2 = 160
!  nr3 = 480
/
&ELECTRONS
  electron_maxstep = 500
  diagonalization = 'david'
  conv_thr =  1.0d-10
  mixing_beta = 0.70
/
&IONS
  ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
   C12.0107   C.wc-n-kjpaw_psl.1.0.0.UPF
   H1.0079H.wc-kjpaw_psl.1.0.0.UPF
   O15.99900  O.wc-n-kjpaw_psl.1.0.0.UPF
   P30.973761 P.wc-n-kjpaw_psl.1.0.0.UPF
   S32.0600   S.wc-n-kjpaw_psl.1.0.0.UPF
  Ti   47.86700  Ti.wc-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Ti   0.0   0.0   0.0263160000   0   0
Ti   0.67000   0.0   0.0263160000   0   0
Ti   0.33000   0.0   0.0263160000   0   0
Ti   0.17000   0.5   0.0263160000   0   0
Ti   0.5   0.5   0.0263160000   0   0
Ti   0.83000   0.5   0.0263160000   0   0
Ti   0.000824658   0.992331197   0.264938249
Ti   0.334135046   0.995049704   0.264624893
Ti   0.667613401   0.992398327   0.264893895
Ti   0.168926625   0.489197175   0.261993802
Ti   0.499777376   0.489341171   0.261832125
Ti   0.834286595   0.493562288   0.264858957
Ti   0.57357   0.987892876   0.144759568
Ti   0.333795375   0.994450512   0.144007883
Ti   0.667723487   0.987841633   0.144749798
Ti   0.167624322   0.486336635   0.144288179
Ti   0.833927173   0.487390518   0.144773288
Ti   0.500148725   0.486358394   0.144260258
Ti   0.000460100   0.237804472   0.170484800
Ti   0.667233312   0.237885209   0.170448961
Ti   0.333852171   0.235526018   0.175041344
Ti   0.168398115   0.741530329   0.169439965
Ti   0.499182489   0.741792231   0.169370400
Ti   0.833844439   0.738095532   0.170226827
Ti   0.0   0.25000   0.060000   0   0
Ti   0.33000   0.25000   0.060000   0   0
Ti   0.67000   0.25000   0.060000   0   0
Ti   0.17000   0.75000   0.060000   0   0
Ti   0.83000   0.75000   0.060000   0   0
Ti   0.5   0.75000   0.060000   0   0
Ti  -0.000849135   0.241620902   0.283991654
Ti   0.334211578   0.229486912   0.294789499
Ti   0.669259871   0.241661770   0.283943878
Ti   0.167941078   0.743027462   0.282833203
Ti   0.500298838   0.743518834   0.282674577
Ti   0.834126861   0.742296000   0.283914549
O0.0   0.792604000   0.0505730000   0   0
O0.67000   0.792604000   0.0505730000   0   0
O0.33000   0.792604000   0.0505730000   0   0
O0.1

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

[Pietro Davide Delugas]

Hello

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

So  normal DOS is

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

The projected density of states is

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

Hope this helps
Best regards, Pietro

Sent from Mail for Windows

From: KRISHNENDU MUKHERJEE
Sent: Wednesday, November 30, 2022 11:23 AM
To: users
Subject: [QE-users] Parallelization and Input/Output of wfc in QE


Dear Dr. Pietro,

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

Thank you,
Best regards,
Krishnendu

---

Dear Krishnendu,

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

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

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

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

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

Best wishes,
Pietro

---

Pietro Bonfà
Università di Parma


On 11/29/22 12:56, KRISHNENDU MUKHERJEE wrote:
>
> How many G-vectors are required to describe a plane-wave ?
>
> It will be very helpful if I could understand the following part of the
> output that I am getting almost in the beginning.
>
> G-vector sticks info
>   
>   sticks:   dense  smooth PW G-vecs:dense   smooth  PW
>   Sum61813093885   364637   128843   20341
>
> Thank you,
> Regards,
>
> Krishnendu
>
> --
>
> Actually, all the coefficients of all the wavefunctions AT A GIVEN K
> POINT: there is one wavefunction file per k point.
>
> Paolo
>
> On 11/28/22 14:07, Riccardo Piombo uniroma1 via users wrote:
>>/So in a single file QE stores ALL the coefficients of ALL the wfcs? />//>/Is 
>>it correct? />//>//>/Thanks for your help, />//>/Riccardo Piombo />//




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[QE-users] R: Why I can not reproduce ferromagnetic fcc Ni in QE 7.1

[Pietro Davide Delugas]

hello
you may have a look at this tutorial.

https://gitlab.com/QEF/materials-for-max-qe2021-online-school/-/archive/master/materials-for-max-qe2021-online-school-master.tar.gz?path=Day-7

Exercise 3 deals with fcc Ni.
Hope it can be useful
Pietro


Da: users  per conto di Jibiao Li 

Inviato: giovedì 17 novembre 2022 06:54
A: users 
Oggetto: [QE-users] Why I can not reproduce ferromagnetic fcc Ni in QE 7.1

Dear all,

I try to perform vc-relax calculations for simple fcc Ni structure, but qe gave 
a nonmagnetic state in the relaxed outcome, with nearly zero magnetic moments 
for all atoms. Is it a well-known problem or simply incorrect input of my 
calculations?

 Magnetic moment per site  (integrated on atomic sphere of radius R)
 atom   1 (R=0.248)  charge= 15.9059  magn=  0.0003
 atom   2 (R=0.248)  charge= 15.9059  magn=  0.0003
 atom   3 (R=0.248)  charge= 15.9059  magn=  0.0003
 atom   4 (R=0.248)  charge= 15.9057  magn= -0.0012

Can anyone tell me how to get a ferromagnetic structure for fcc Ni in QE 7.1?


Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 
54944118000

Web of Science Research ID: 
F-1905-2016

 &CONTROL
 calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
  outdir = './' ,
  pseudo_dir = '/home/jibiaoli/pseudo/PAW' ,
  prefix = 'bulk' ,
   nstep = 99 ,
 /
 &SYSTEM
   ibrav = 1,
   celldm(1) = 6.58,
 nat = 4,
ntyp = 1,
 ecutwfc = 49 ,
 ecutrho = 451 ,
   input_dft = 'sla+pw+ggx+vdw1' ,
 occupations = 'smearing' ,
 degauss = 0.02D0 ,
smearing = 'methfessel-paxton' ,
   nspin = 2,
   starting_magnetization(1) = 0.6,
 /
 &ELECTRONS
electron_maxstep = 299,
 mixing_beta = 0.2D0 ,
 diagonalization = 'david' ,
 /
 &IONS
ion_dynamics = 'bfgs' ,
 /
 &CELL
   cell_dynamics = 'bfgs' ,
 cell_dofree = 'ibrav' ,
 /
ATOMIC_SPECIES
   Ni   58.71  Ni.pbe-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
   Ni  0.00.50.5
   Ni  0.50.00.5
   Ni  0.50.50.0
   Ni  0.00.00.00  0  0
K_POINTS automatic
  9 9 9   0 0 0








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[QE-users] R: Quantum espresso 7.1

[Pietro Davide Delugas]

Hello
The error might be due to a bug that has been fixed one month ago. The fix will 
be present in the next release.
In the meantime,  if you are using v7.1, you can apply the fix using the patch 
in attachment and recompile pw
to apply the patch, you can use the patch command like this:

patch -p1 < patch.diff

best regards
Pietro


Da: users  per conto di Tom Demeyere 

Inviato: mercoledì 26 ottobre 2022 16:45
A: Quantum ESPRESSO users Forum 
Oggetto: Re: [QE-users] Quantum espresso 7.1

Dear Maria,

I got this error a few weeks back when trying to run a calculation with ibrav = 
-13 on 7.1. I ended up using 7.0 where the problem does not occur

-
Tom Demeyere MSc
PhD student
Skylaris Research Group
School of Chemistry, University of Southampton

On 26 Oct 2022, at 15:05, Maria Fumanal Quintana  wrote:





patch.diff
Description: patch.diff
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[QE-users] R: security code for downloading QE

[Pietro Davide Delugas]

Hi Giuseppe
it should be just above, the request a 3 figure number
Pietro

Da: users  per conto di Giuseppe 
Mattioli 
Inviato: martedì 20 settembre 2022 16:19
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] security code for downloading QE


Dear all
I'm experimenting some problems when downloading QE as registered
user... What is and Where can I get the "security code" asked when I
try to log in?
Thank you in advance
Giuseppe


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

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[QE-users] R: CP example 08

[Pietro Davide Delugas]

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

K_POINTS gamma

​best regards - Pietro

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


Dear Expert,

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

Regards,
Krishnendu


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[QE-users] R: Molecular dynamics calculation crashing

[Pietro Davide Delugas]

Dear Elio

a  few  usual  things to check are:

  *   the positions and lattice description  in the supercell input. A quick 
glance with xcrysden is usually enough
  *the value of the initial forces ( if the issue occurs after the first 
step)
  *   that you have set up correctly occupations, smearing and the density of  
k-point mesh.

Apart from those it's difficult to give any other suggestion without seeing the 
input.
best regards
Pietro


Da: users  per conto di Elio Physics 

Inviato: lunedì 8 agosto 2022 03:02
A: Quantum Espresso users Forum 
Oggetto: [QE-users] Molecular dynamics calculation crashing

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:


  1.  My ecutwfc is already high (130Ry).
  2.   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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[QE-users] R: Translated orbitals in periodic calculation

[Pietro Davide Delugas]

Dear Philip

Final orbitals corresponding  to degenerate set of levels may always be 
different sets of wavefunctions spanning the same manifold.
This may happen for a lot of reasons (e.g. a different number of MPI ranks, 
using a different diagonalization algorithm).

In your case the reason may be that you are running using a different set of 
symmetries in the 2 cases.

In supercell calculations, all symmetries that include a fractional translation 
are disabled.
This makes the program exclude more symmetries in the second setup ( the 3 
symmetry equivalent k points in the second run are points that are symmetry 
equivalent only using operations that have been excluded).

To avoid symmetrisation, and possibly (not warranted though) end up with the 
same orbitals you may use the &system flags:

nosym = .true.

or the safer

nosym_evc = .true.

I hope it works, but it's not guaranteed that you will obtain the same set of 
orbitals even without symmetries.
best regards
Pietro

Da: users  per conto di Phillip 
Thomas 
Inviato: martedì 2 agosto 2022 03:03
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Translated orbitals in periodic calculation

Dear QE team,

I have an issue regarding orbitals generated from QE 7.0 runs on two different 
translated variants of a Silicon lattice. I am using a primitive cubic cell 
containing 8 atoms instead of the simplest 2-atom unit cell (as I need to pass 
the output orbitals to another program which only accepts a tetragonal cell 
geometry).

Here is the input file for 'pw.x' for the first variant:

&control
   prefix = 'silicon'
   calculation = 'scf'
   tstress = .true.
   etot_conv_thr = 1d-5
   forc_conv_thr = 1d-4
/
&system
   ibrav = 1
   celldm(1) = 10.173697855629921
   nat = 8
   ntyp = 1
   nbnd = 32
   ecutwfc = 80.0
/
&electrons
   electron_maxstep = 100
   conv_thr = 1.0d-8
   mixing_mode = 'plain'
   mixing_beta = 0.7
   mixing_ndim = 8
   diagonalization = 'david'
   diago_david_ndim = 4
   diago_full_acc = .true.
/
&ions
/
ATOMIC_SPECIES
  Si  28.086  Si.pw-mt_fhi.UPF
ATOMIC_POSITIONS alat
  Si  0.00  0.00  0.00
  Si  0.00  0.50  0.50
  Si  0.50  0.00  0.50
  Si  0.50  0.50  0.00
  Si  0.25  0.25  0.25
  Si  0.75  0.75  0.25
  Si  0.25  0.75  0.75
  Si  0.75  0.25  0.75
K_POINTS automatic
4 4 4 0 0 0

The second variant has the same input file except that the coordinates of the 
atoms are shifted to:

  Si  0.125  0.125  0.125
  Si  0.125  0.625  0.625
  Si  0.625  0.125  0.625
  Si  0.625  0.625  0.125
  Si  0.375  0.375  0.375
  Si  0.875  0.875  0.375
  Si  0.375  0.875  0.875
  Si  0.875  0.375  0.875

Both calculations give the same total energy, -63.52598191 Ry, as I would 
expect, and the same band structure (except that three additional symmetry 
equivalent bands are printed out in the latter case); the bands for matching 
KPOINTS are also the same in both runs, all as expected. Here are the bands for 
the 0 0 0 KPOINT for reference:

 End of self-consistent calculation

  k = 0. 0. 0. ( 12797 PWs)   bands (ev):

-5.8606  -1.6207  -1.6207  -1.6207  -1.6207  -1.6207  -1.6207   3.3705
 3.3706   3.3706   3.3706   3.3706   3.3706   6.2827   6.2827   6.2827
 6.8712   6.8712   6.8712   6.8712   6.8712   6.8712   8.8517   8.8517
 8.8517   9.6765  14.0241  14.0783  14.0783  16.4618  16.4618  16.4618

Now I would like to generate the orbitals for the 0 0 0 KPOINT in cube file 
format, so here is my input to ''pp.x':

 &inputpp
 prefix='silicon'
 plot_num=7
 kband(1)=1
 kband(2)=  32
 kpoint=1
 lsign=.true.
 /
 &plot
 iflag=3
 output_format=6
 /


When I visually inspect the orbitals, I find that many of the orbitals are 
qualitatively different for the two translated variants of the lattice; they 
are not simply translated variants of the same orbital as I would expect. I 
have attached plots of the highest occupied orbital (#16) as examples.

So I am curious, is there a mistake in my inputs or procedure that would cause 
differences like these? If not, then is there a way in QE that I can generate 
the orbitals such that they are translationally invariant? Many thanks for 
looking into this!

Kind regards,

Phillip Thomas, Ph.D.
National Energy Research Scientific Computing Center
Lawrence Berkeley National Laboratory
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[QE-users] R: Advanced Quantum ESPRESSO tutorial: Hubbard and Koopmans functionals from linear response

[Pietro Davide Delugas]

maybe just the first lines of the mailing-list announcement could go. Is it ok ?


Da: users  per conto di Iurii TIMROV 
via users 
Inviato: venerdì 29 luglio 2022 11:02
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] Advanced Quantum ESPRESSO tutorial: Hubbard and Koopmans 
functionals from linear response


Dear Quantum ESPRESSO community,


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


Dates: 9-11 November 2022

Format: Online

Registration fee: 0 (free of charge)

Deadline for applications: 1 October 2022

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


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


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


Keynote speakers:

Leoor Kronik (Weizmann Institute 
of Science, Israel)

Renata Wentzcovitch 
(Columbia University, USA)

Matteo Gatti (École Polytechnique, 
France)


Lecturers:

Nicola Marzari (EPFL and PSI, 
Switzerland)

Giovanni Pizzi (EPFL and PSI, 
Switzerland)

Edward Linscott (EPFL, Switzerland)

Iurii Timrov (EPFL, Switzerland)

Nicola Colonna (PSI, 
Switzerland)

Andrea Floris (Lincoln University, UK)

Andrea Ferretti (CNR Modena, Italy)


Matteo Cococcioni 
(University of Pavia, Italy)



Yours sincerely,

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


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[QE-users] R: bands.x output incomplete

[Pietro Davide Delugas]

Dear Kenneth

You are using a very old version of pw.x.  For those versions wave functions 
were saved by default in the non-collected format, and it was possible to read 
them only by running the post-processing apps such as bands.x using exactly the 
same number of MPIs. What the error message is suggesting you is to rerun pw.x 
with the option wf_collected=.true. that would make the program save the data 
in the collected format making them readable by the post-processing in any case.

I suggest, if possible, using a more recent version of pw where this behavior 
has been corrected and binary data are always saved in collected formats.

Thanks for postiong your question. For the future try to avoid too large 
attachments. By the rule messages should not exceed a size of  200Kb.

Best regards and greetings
Pietro

Da: users  per conto di SK 

Inviato: domenica 24 luglio 2022 15:00
A: users@lists.quantum-espresso.org 
Oggetto: [QE-users] [SPAM] bands.x output incomplete

Hello,

Kindly help me clarify this.

I was running bands.x for Cs2AgBiBr6 and was getting an error that suggested: 
"wf_collect=.true." should be set. (i.e when I run without mpirun but same run 
incompletely when I use mpirun.):

bands.x < bandsOrig.in > bandsOrig.out---   [wf_collect=.true. 
error]

mpirun -np 7 --oversubscribe bands.x < bandsOrig.in > bandsOrig.out
---[runs but output indicated incomplete run]

I re-run the pw.x for bands with wf_collect=.true. included in &CONTROL card.

Now whether with mpirun or not, bands.x gives no error but output file 
indicates it did not terminate properly. What I mean by incomplete is the 
output file did not have "JOB DONE." at the end, it stopped at the line: 
negative rho (up, down):  4.106E-02 0.000E+00

Attached are my input and output files for scf, nscf, bands and bands.x and 
info on CPU and RAM

I am running v.5.1 of QE.

Thank you and would very much appreciate some assistance.


Regards

Kenneth Sandinah

Graduate student

University of Ghana


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Re: [QE-users] extrapolated charge too large during vc-relax leading to too many energy bands not converged error

[Pietro Davide Delugas]

Dear Lucian

I would first try setting
pot_extrapolation='none' in the electrons namelist. If the problem is 
caused by the extrapolation this should make it go away.


for the calculation with vacuum I would also set

cell_dofree='ibrav+2Dxy'

hope this can solve your problem

best regards
Pietro


On 7/25/22 21:45, Lucian D. Filip wrote:

Hello all,

I have stumbled on a problem that is very frustrating and cannot 
figure out what is happening. I am trying to do a vc-relax of a rather 
large structure 115 atoms. It constits of 
3-SrRuO3/7-PbTiO3/3-SrTiO3/7-PbTiO3/3-SrRuO3. The numbers in front of 
the materials represent the number of unit cells of each material. The 
structure is 1x1x23. I have tried both with vacuum on either side 
(about 15 A because if I add more then the FFT limit is reached and I 
get that error) and in super cell configuration (i.e. no vacuum) but 
the same thing happens:


The calculation starts  and the first scf step converges in 240 
iterations. I know it is a large number but the structure is also 
large and I have seen that this is quite common for these cases. I may 
be wrong thou... The starting charge is  951.8694, renormalised to 
952.. All is good and the first step converges. Then in the second 
step starts the weird part:


extrapolated charge  991.00311, renormalised to  952.0

Then it tries to perform the first scf step and the calculation dies 
with the:


Error in c_bands(1):

too many bands are not converged

I do not understand what is happening because I have succesfully 
relaxed slightly smaller but similar structures: 
3-SrRuO3/7-PbTiO3/3-SrTiO3/3-SrRuO3 and 3-SrRuO3/7-PbTiO3/3-SrRuO3. 
These two I relaxed with 15A of vacuum on either side.



I am using ultrasoft PBE PPs.

Here is the input I used:


&control
 calculation = 'vc-relax'
 restart_mode    = 'from_scratch'
 prefix  = '10Fd-3i-10Fd-slab'
 disk_io = 'low'
 tstress = .true.
 tprnfor = .true.
 etot_conv_thr   = 1.e-4
 forc_conv_thr   = 1.e-4
 verbosity   = 'high'
 pseudo_dir  = '../pp/pbe-US/'
 outdir  = '10Fd-3i-10Fd-slab'
 nstep   = 600
/

&system
 ibrav   = 6
 celldm(1)   = 7.37937998548
 celldm(3)   = 28.8910838525
 nat = 115
 ntyp    = 5
 ecutwfc = 60.
 ecutrho = 480.
 occupations = 'smearing'
 degauss = 0.01
 smearing    = 'gaussian'
/

&electrons
 diagonalization = 'david'
 mixing_beta = 0.1
 mixing_mode = 'local-TF'
 conv_thr    = 1.e-8
 scf_must_converge   = .false.
 electron_maxstep    = 400
/

&ions
 ion_dynamics    = 'bfgs'
/

&cell
 cell_dynamics   = 'bfgs'
/

ATOMIC_SPECIES
 Pb    1  Pb.pbe-dn-rrkjus_psl.0.2.2.UPF
 Ti    1  Ti.pbe-spn-rrkjus_psl.1.0.0.UPF
 O 1   O.pbe-n-rrkjus_psl.0.1.UPF
 Sr    1  Sr.pbe-spn-rrkjus_psl.1.0.0.UPF
 Ru    1  Ru.pbe-n-van.UPF

ATOMIC_POSITIONS {angstrom}
Sr  0.00    0.00    0.00
O   1.952500    1.952500    0.00
Ru  1.952500    1.952500    1.952500
O   0.00    1.952500    1.952500
O   1.952500    0.00    1.952500
Sr  0.00    0.00    3.905000
O   1.952500    1.952500    3.905000
Ru  1.952500    1.952500    5.857500
O   0.00    1.952500    5.857500
O   1.952500    0.00    5.857500
Sr  0.00    0.00    7.81
O   1.952500    1.952500    7.81
Ru  1.952500    1.952500    9.762500
O   0.00    1.952500    9.762500
O   1.952500    0.00    9.762500
Pb  0.00    0.00    11.7202344916000
O   1.952500    1.952500    12.1688551695000
Ti  1.952500    1.952500    13.9438177707000
O   0.00    1.952500    14.2579079188000
O   1.952500    0.00    14.2579079188000
Pb  0.00    0.00    15.8398546661000
O   1.952500    1.952500    16.2884753441000
Ti  1.952500    1.952500    18.0634379452000
O   0.00    1.952500    18.3775280934000
O   1.952500    0.00    18.3775280934000
Pb  0.00    0.00    19.9594748407000
O   1.952500    1.952500    20.4080955187000
Ti  1.952500    1.952500    22.1830581198000
O   0.00    1.952500    22.4971482679000
O   1.952500    0.00    22.4971482679000
Pb  0.00    0.00    24.0790950152000
O   1.952500    1

Re: [QE-users] problems with DFT+U+V (No atom equivalent to r2 error)

[Pietro Davide Delugas]

This last issue has been fixed in the current release candidate:

https://gitlab.com/QEF/q-e/-/tree/qe-7.1-rc2

Pietro

Il 9 giu 2022 6:54 AM, Corina Urdaniz  ha scritto:
Thank you very much for your quick answer and for your time. I read the paper 
carefully.

Just as a comment, I tried the system: an atom of V on mgo, and I called the 
oxygen below the V as O1, but it didn't work either with eps=5.d-6.
ATOMIC_SPECIES
V   50.9415   v_pbe_v1.4.uspp.F.UPF
O1 15.999   O.pbe-nl-kjpaw_psl.1.0.0.UPF
Mg 24.305   Mg.pbe-n-kjpaw_psl.0.3.0.UPF
O  15.999   O.pbe-nl-kjpaw_psl.1.0.0.UPF
$(cat positions)
K_POINTS automatic
1 1 1 0 0 0

HUBBARD (ortho-atomic)
V V-3d V-3d  1 1 1.2
V V-3d V-4s  1 1 0.5
V V-3d O1-2p 1 2 2
V V-4s V-4s  1 1 0.5

I applied your suggestion, I changed the eps  to "eps=5d-5" and it works 
perfectly!..but... at the end of scf.out I get:
.
convergence has been achieved in  19 iterations

 Writing all to output data dir ./tmp/MgO.save/
 Message from routine qexsd_init:hubbard_v:
 XML printout for hubbard_v with background channels is not implemented

 %%
 Error in routine qexsd_init_dft: (1):
 Internal error: second Hubbard channel is present but hubb_n2 or hubb_l2 
or U2 is not present
 %%




thank you very much

all the best,


Corina.




IBS Center for Quantum Nanoscience
Seoul, South Korea


On Wed, Jun 8, 2022 at 8:54 PM Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

Dear Corina,


Please do not forget to indicate your affiliation.


You are trying to model a V-O dimer, right? Note that DFT+U+V was designed for 
periodic solids. Also note that a virtual 3x3x3 supercell is created in DFT+U+V 
to find the indices of neighboring atoms to assign the inter-site Hubbard V 
interaction (please see the discussion on page 11 in this paper: 
arXiv:2203.15684).


In order to solve your problem just change the value of the parameter "eps" to 
e.g. 5.d-5 in PW/src/intersite_V.f90 and then recompile the code. Note that the 
default value "eps = 5.d-6" works in the majority of cases (at least for 
periodic solids).


HTH


Greetings,

Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334

From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Corina Urdaniz 
Sent: Wednesday, June 8, 2022 5:24:24 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] problems with DFT+U+V (No atom equivalent to r2 error)

Dear All, i'm new in QE, i running  DFT+U+V in simple system (see input below), 
 and i obtain this error message:

I diff > 0, diff=1.00  at1=1 at2=1

 %%
 Error in routine symonpair (1):
 No atom equivalent to r2
%%

 I'm running too in the new development version and I obtain the same error.

&control
calculation = "scf"
prefix = "xxx"
pseudo_dir = "xx"
outdir = "./tmp"
restart_mode = "from_scratch"
nstep = 500
/
&system
  ibrav=6,
  A=12.375
   C= 29
   nat=2,
   ntyp=2,
   ecutwfc =70,
   ecutrho= 600,
occupations='smearing',
smearing='mv'
degauss=0.005
starting_magnetization(1)=0.7
starting_magnetization(2)=-0.07
vdw_corr = 'grimme-d3'
nspin=2
lda_plus_u = .true.
lda_plus_u_kind = 2
U_projection_type = 'ortho-atomic',
Hubbard_V(1,1,1)=1
Hubbard_V(1,2,2)=2
/
&electrons
electron_maxstep = 500,
conv_thr = 1.0D-8,
mixing_beta = 0.3,
/
&IONS
/
ATOMIC_SPECIES
V   50.9415   v_pbe_v1.4.uspp.F.UPF
O  15.999   O.pbe-n-kjpaw_psl.0.1.UPF
ATOMIC_POSITIONS (angstrom)
V5.15504564855.1550098098   14.1845777826
O5.15499766745.1549967180   12.0833856727
K_POINTS automatic
1 1 1 0 0 0

for the new development i try with this card:
HUBBARD (ortho-atomic)
V V-3d V-3d1 1 1.2
V V-3d V-4s1 1 0.5
V V-3d O-2p   1 2  2
V V-4s V-4s1 1  0.5


the problem was  solved when i changed the coordinates  to something like:

ATOMIC_POSITIONS (angstrom)
V 0.0 0.0 0.0
O 0.0 0.0 2.0



but I get the same error as above if I use the positions from relax.out

Is it a bug, or is it just the question of some parameter tweaking?


TIA!

all the best,

Corina.
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[QE-users] R: molecule dismantled during 'relax'

[Pietro Davide Delugas]

Hello

I would check first if in the output there is any warning about the accuracy of 
the forces; it may happen if the convergency threshold is too hight.

Pietro




Da: users  per conto di Elio Physics 

Inviato: venerdì 13 maggio 2022 22:36
A: Quantum Espresso users Forum 
Oggetto: [QE-users] molecule dismantled during 'relax'

Dear QE users,

I am relaxing a molecule in QE. I have used a vacuum distance of 13A in all 
directions and the flag assume_isolated='martyna-tuckerman'. I have also added 
the Van der Waals corrections.
Other than endless fluctuations in the forces,  the molecule got distorted and 
some atoms "flew away" after a few steps of relaxation.

Any thoughts of how to remedy this situation?

Regards

Elie Moujaes
Adjunct professor
Federal University of Rondonia
Porto Velho
Brazil





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Re: [QE-users] Alpha_mix not resolving ph.x convergence failure

[Pietro Davide Delugas]

Hello
many times it works better if you reduce alpha_mix gradually. For 
example with


alpha_mix(10) = 0.3

and

alpha_mix (15) = 0.1

you use default value for alpha_mix in first 10 iterations, then  you 
reduce it to 0.3, and to 0.1 after 15th iteration.


Pietro

On 5/13/22 00:06, Jessica Johnson wrote:

Hello QE users,

I am having trouble converging a phonons calculation. The archives 
indicate that many users were able to solve this problem reducing the 
default value of alpha_mix(1) to .1 or .2. I have tried many values 
from .01 - .9 and I end up with the calculation being unable to 
converge. In addition, I have lowered the convergence threshold for 
the scf calculation thinking that would set up the phonons calculation 
to converge more easily. I have also varied the nq1, nq2, k1 and k2 
values. Neither of the latter two changes made much difference


I am using espresso + d3q (version number I am unsure of, however the 
release date is Dec. 12, 2021).


My ultimate goal is to use the d3_q2r.x and d3_qha.x executables to 
compute adsorption of H onto MoS2 layers.


Here are my pw.x and ph.x input files for H adsorbed onto the Mo site:


&CONTROL
   calculation     =  'scf'
   prefix          =  '1T_H_Mo_0'
   pseudo_dir      =  '.'
   title           =  '1T layers'
   verbosity       =  'high'
 /

 &SYSTEM
   A               =  6.385866
   B               =  6.385866
   C               =  14
   cosAB           =  -0.5
   cosAC           =  0
   cosBC           =  0
   degauss         =  0.005
   ecutrho         =  368
   ecutwfc         =  92
   ibrav           =  4
   input_dft       =  'BEEF-vdW'
   nat             =  13
   ntyp            =  3
   occupations     =  'smearing'
   smearing        =  'gaussian'
 /

 &ELECTRONS
   conv_thr        =  1e-10
 /

 &IONS
 /

 &CELL
   cell_dofree     =  'epitaxial_ab'
 /

ATOMIC_SPECIES
  Mo    95.95   Mo_HER.upf
  S    32.066   S_HER.upf
  H    1.00794   H_HER.upf


ATOMIC_POSITIONS crystal
Mo            0.01       -0.01  0.2432527978
S             0.3387936710        0.1693960855  0.1415931532
S             0.1716523937        0.3433032874  0.3652990281
H            -0.005000        0.00  0.3685376338
Mo            0.4770138961       -0.0459752078  0.2481206178
S             0.8306049145        0.1693960855  0.1415931532
S             0.67        0.325000  0.3420643699
Mo            0.4770138961        0.5229861039  0.2481206178
S             0.8306049145        0.6612073290  0.1415931532
S             0.6566962126        0.8283471063  0.3652990281
Mo            0.0459752078        0.5229861039  0.2481206178
S             0.345000        0.665000  0.1232508011
S             0.1716523937        0.8283471063  0.3652990281

K_POINTS automatic
  4   4   1   0   0   0

_


Phonon calculation 1T_H_Mo_0

&inputph
  prefix        = '1T_H_Mo_0'
  fildyn        = '1T_H_Mo_0.1.G'
  tr2_ph        = 1.0d-14
  alpha_mix(1)  = .1
  ldisp         = .true.
  nq1           = 4
  nq2           = 4
  nq3           = 1
/

___

Thank you in advance for your help on this matter, as it is one of the 
tougher ones I have encountered using QE.


Jessica Johnson
graduate student
Materials Science and Engineering Department
Rutgers University, New Brunswick, New Jersey

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[QE-users] R: Advice for Parallel Execution

[Pietro Davide Delugas]

Hello
The size of your system is such that parallel execution should be beneficial 
for up to 50, 60 MPI ranks, without any further option. If you are planning to 
use something like 200 cores the simplest and yet effective way to go would be 
to use an executable compiled with hybrid MPI + OpenMP parallelism and run it 
with 4 OpenMP threads.

About your test in the 8 core machines, looking at your output, it seems to me 
that you are using a multithreaded linear algebra library.
If it is the case you should make sure that the number of MPI ranks times the 
number of threads doesn't exceed the number of cores.  8 in your case. To set 
the number of openMP threads you need to specify the OMP_NUM_THREADS 
environment variable. e.g.
export OMP_NUM_THREAD=2   if you run with 4 MPIs
or
export OMP_NUM_THREADS=1 if you run with 8 MPIs

hope this helps, best regards -- Pietro

Da: users  per conto di Robert 
Fleming 
Inviato: mercoledì 13 aprile 2022 16:36
A: Quantum ESPRESSO users Forum 
Oggetto: [QE-users] Advice for Parallel Execution

Greetings,

I’m running scf calculations on an amorphous Si surface terminated with 
different functional groups (input file attached for context), and I’m 
experiencing poor scaling behavior in parallel.  I’m running these jobs locally 
on an 8-core CPU to test before scaling up the system size to an hpc cluster.

I’ve noticed that increasing the number of MPI processes from 4 to 8 (mpirun -n 
4 pw.x -in [myscript] vs. mpirun -n 8 pw.x -in [myscript]) results in the job 
taking longer (~ 1hr vs. 1.5 hr).  Looking through the documentation, I see 
that there are several command line switches for different levels of 
parallelization beyond just the number of MPI processes.  While it’s possible 
that my system size is potentially too small to benefit from parallel execution 
(24 atoms, 103 electrons), I think it’s probably more likely that I’m not 
appropriately taking advantage of these.

Would anyone be willing to share some advice or “rules of thumb” on the best 
way to select these parallelization levels for small-to-medium sized jobs (say, 
an 8 core CPU vs. 150-200 processors on an hpc platform)?

Thank you,

Robert “Drew” Fleming, Ph.D.
Assistant Professor of Mechanical Engineering
College of Engineering & Computer Science
Arkansas State University
(870) 972-3743
roflem...@astate.edu






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Re: [QE-users] Failure in installing QE 6.7 in a server

[Pietro Davide Delugas]

hello

when you compile the qe, first the program creates all executables in 
bin subdirectory of the top qe directory. Check if they are there.


If they are:  you may either avoid the secod step either using  the full 
path to execute the program.


e.g. in my case

/home/pietro/q-e/bin/pw.x

or adding  to the q-e/bin directory to the default path. For example in 
my case:


type the bash command

export PATH=/home/pietro/q-e/bin:$PATH

The second installationt would be copying the executables in a specified 
directory, that, if I am not wrong,  by default is /usr/local/bin  for 
which you would need the administrator privileges.



The second thing you tried has nothing to do with the compilation of the 
package.


It's ubuntu that knows that there is a debian package of 
quantum-espresso available, and asks you if you want to install it. But 
again to do this you need administrator privileges.



hope it helps

best regards -- Pietro




On 4/4/22 03:14, Jeffrey Tanudji wrote:

Dear all QE users,


I believed I had successfully installed QE 6.7 in a server, but when I 
tried to run pw.x, it stated


bash: pw.x: command not fou
Install package 'quantum-espresso' to provide command 'pw.x'? [N/y]


However, when I entered y, the result was an error saying failed to 
obtain authentication. Since I am new to Linux, I did a search on 
google about this problem and most of the forum mentioned was about 
"Fedora" and nothing about quantum espresso. If anybody knows of any 
solution to this problem, your help will be greatly appreciated.



Best regards,


Jeffrey TANUDJI

Graduate student

Department of Applied Physics

Osaka University

Suita, JAPAN


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[QE-users] R: qe-gpu 7.0 - compilation issue (MKL not detected)

[Pietro Davide Delugas]

dear Giovanni
you could  try just adding the /.../mkl/lib/intel64/ to the LD_LIBRARY_PATH or
source of the /mkl//env/vars.sh script and then running the configure 
script

Hope this solves your problem
greetings
Pietro

Da: users  per conto di Giovanni 
Cantele 
Inviato: martedì 8 marzo 2022 12:46
A: Quantum ESPRESSO users Forum 
Oggetto: [QE-users] qe-gpu 7.0 - compilation issue (MKL not detected)

Dear all,

I’m trying to configure the compilation of qe-7.0 on GPUs. I’m using the 
following script to launch configure:
---
export VERSION=21.3
export VERSION=20.11
export CUDA_VERSION=11.1

export NVHPC=/nfsexports/nvidia/hpc_sdk

nvcudadir=$NVHPC/Linux_x86_64/$VERSION/cuda
nvcompdir=$NVHPC/Linux_x86_64/$VERSION/compilers
nvmathdir=$NVHPC/Linux_x86_64/$VERSION/math_libs
nvcommdir=$NVHPC/Linux_x86_64/$VERSION/comm_libs

export OPAL_PREFIX=$nvcommdir/mpi

export MANPATH=$MANPATH:$nvcompdir/man

PATH=$nvcudadir/bin:$nvcompdir/bin:$nvcommdir/mpi/bin:$PATH
export PATH

CPATH=$nvcudadir/include:$nvmathdir/include:$nvcommdir/mpi/include:$nvcommdir/nccl/include:$nvcommdir/nvshmem/include:$CPATH
export CPATH

LD_LIBRARY_PATH=$nvcudadir/lib64:$nvcompdir/lib:$nvmathdir/lib64:$nvcommdir/mpi/lib:$nvcommdir/nccl/lib:$nvcommdir/nvshmem/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
. /nfsexports/intel/oneapi/mkl/latest/env/vars.sh

export OMPI_FC=nvfortran
export CUDA_HOME=$nvcudadir/$CUDA_VERSION

./configure --enable-openmp  --with-cuda=$CUDA_HOME --with-cuda-cc=70 
--with-cuda-runtime=11.1 --without-scalapack -with-cuda=yes 
--enable-cuda-env-check=no
---


Now, the problem is that I’m not able to make configure to recognise Intel MKL 
(2021.1.1 version).

The correct line to link to them is
 -L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_pgi_thread -lmkl_core 
-pgf90libs -mp -lpthread -lm -ldl
and adding
 -i8  -I"${MKLROOT}/include”
to the compiler options.

However, if I try to run the above configure command adding
LDFLAGS=“-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_pgi_thread -lmkl_core 
-pgf90libs -mp -lpthread -lm -ldl”
the configure stops finding the cuda enviroment, selects gfortran as compiler 
and exits with error. On the other hand, if I skip LDFLAGS (but
with MKLROOT correctly set up), the cuda environment is correctly detected but 
MKL are not automatically detected.

Could you please check the above script and, possibly, give any hint useful to 
solve the issue?

I thank you all in advance.

Giovanni



--

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: https://sites.google.com/view/giovanni-cantele/home

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Re: [QE-users] Regarding pseudopotentials...

[Pietro Davide Delugas]

Hello

hopefully soon in the main site.
In the meantime here

pseudopotentials.quantum-espresso.org




Il 27 gen 2022 6:50 AM, abhijith vg  ha scritto:
Dear espressionists,

I am not able to find pseudopotential library on the website. Where I can find 
them..?

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Re: [QE-users] atomic code Ver 6.2.2

[Pietro Davide Delugas]

Dear Mahmoud

Unfortunately the 6.2.2 version of QE was not tagged ( we were in the 
transition between svn and git ), but there were no changes in atomic 
code between 6.2.1 and 6.2.2. Yonu may download that version here ( 
https://gitlab.com/QEF/q-e/-/releases/qe-6.2.1  ).
The use_xsd flag is uised to chose between the legacy UPF format and the 
new one that is compliant to XMLSchema descripion. The pseudos are 
completely equivalent for what concerns tha calculations.  Thanks for 
reporting about the missing documentation we will add it a.s.a.p.


best regards and greetings - pietro

On 11/24/21 10:09 AM, Mahmoud Payami Shabestari wrote:

Dear QE Developers and Users,
Hi.
I noticed most of pseudopotentials available in 
https://www.quantum-espresso.org/pseudopotentials 


were generated by atomic code Version 6.2.2.
I would be grateful if a link is provided for its download (if public).
Also, a new logical variable "use_xsd" has been introduced in QE-6.3+, 
but not documented. By a quick search in source files it seems to be 
related to upf formats.

Thank you in advance.
Mahmoud Payami
NSTRI, AEOI, Tehran, Iran
Email: mpay...@aeoi.org.ir
Phone: +98 (0)21 82066504


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Re: [QE-users] info about setting celldm

[Pietro Davide Delugas]

Hello Patrizio
yes it is correct for F.C.C. lattice you need to specify ibrav=2. An 
celldm(1) is the cube's edge length.
As a rule the celldm and also the A,B,C and cosAB, cosBC, cosAC are 
always those of the "conventional" l cell. It means the cube for cubic 
lattices , the tetragonal paralleliped for the
tetragonal lattices and so on. See also the documentation  on ibrav 
https://www.quantum-espresso.org/Doc/INPUT_PW.html#idm199

regards - Pietro

On 11/23/21 3:08 PM, patrizio.grazi...@cnr.it wrote:


Hello everybody,

I'd like to have from you a proof/disproof of my understanding on the 
use of celldm for F space groups.


I read in the instructions that QE uses the primitive cell, in the 
case of Silicon I mean for that the "slanted" cell having parameter 
around 0.387 nm and 60° angles, say like here 
https://www.iue.tuwien.ac.at/phd/ungersboeck/node27.html .


However, in an example for silicon, here 
https://www.quantum-espresso.org/resources/tutorials/shanghai-2013/getting-started/lecture1.pdf 
, I see that in the case of silicon with ibrav = 2 the entered celldm 
correspond to 0.543 nm, the side of the "cubic cell".


Thus, if I'm working with a F space group, ibrav = 2, I must use the 
cube side as celldm, ~ 0.54 nm for silicon. Is this correct?


If I'd like to work with the "slanted primitive cell" with angles of 
60°, which in silicon has lattice constant ~ 0.387 nm, how can I do? I 
apologize but I couldn't find this in any tutorial I found.


Thanks for your time,
Patrizio



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Re: [QE-users] [QE-GPU] Ylm out of bounds

[Pietro Davide Delugas]

Hello
Could you provide more details ?
Regards Pietro

Sent from Mail for Windows

From: Daniel B. Straus
Sent: Tuesday, November 2, 2021 4:09 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] [QE-GPU] Ylm out of bounds

Hello,

Jobs that ran fine with 6.7 are failing in 6.8 with the following error:

%%
 Error in routine  ylmr (6):
 l>4 => out of bounds in Ylm with CUDA Kernel
%%

I am using the containers published at 
https://ngc.nvidia.com/catalog/containers/hpc:quantum_espresso for both 6.7 and 
6.8.

Any ideas?

Thanks,
Daniel

--
Daniel Straus
Postdoctoral Research Associate
Department of Chemistry
Princeton University
Frick Laboratory A09
Princeton, NJ 08544
dstr...@princeton.edu


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Re: [QE-users] Nvidia A100 / Possible implementation

[Pietro Davide Delugas]

Dear Chiara
QE 6.8 ( as well as QE 6.7 ) works fine also on A100.
Best regards Pietro
Sent from Mail for Windows

From: Chiara Biz
Sent: Friday, October 22, 2021 9:44 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Nvidia A100 / Possible implementation

Dear Team of Quantum Espresso,

I hope you all are doing very fine.  In a previous conversation Dr. Spiga 
suggested us to buy Volta and Ampere Architectures to speed up our 
calculations. We followed the advice and we bought a V100 that is making 
wonders (thank you again for the advice!).

We still have budget to use and we would like to buy an Ampere A100 80Gb to fit 
another machine, but we noticed that Quantum Espresso compilation lacks the 
proper architecture signature for the Ampere (even the 6.8 version). We expect 
the Ampere to be a 80 (considering the Volta is a 70), but, my question is, how 
can we implement that??? Is there a way to go? What should we write?

Thanks again for your help. QE works like a charm.

Best regards
Chiara

[cid:image002.png@01D7C77A.9A8EB420]
MagnetoCat SL
Calle General Polavieja 9, 3 Izq
03012 Alicante, Spain
Tel. +34 865593094







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Re: [QE-users] External forces energy

[Pietro Davide Delugas]

Hello
I guess this  is the variation of the potential energy of the external 
field; that is the work done by the external forces with the opposite sign.
If you have started the relaxation from a minimum of the internal 
forces, the external work should be positive and the change in the 
external potential energy negative.


best regards

Pietro


On 10/13/21 12:04 AM, Ronald Cohen wrote:
I am unclear about the External forces energy when adding additional 
ATOMIC_FORCES. In my case these are from an external electric field. 
It seems to me the energy should go up when you add external forces, 
not down, and yet I get


External forces energy = -0.00347627 Ry

Can anyone explain the logic?

Thanks,

Sincerely,

Ron

---
Ronald Cohen
Extreme Materials Initiative
Carnegie Institution for Science
5251 Broad Branch Rd., N.W.
Washington, D.C. 20015
rco...@carnegiescience.edu 
office: 202-478-8937
skype: ronaldcohen
twitter: @recohen3

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Re: [QE-users] qe-6.8 with CUDA compiling unsuccessfully

[Pietro Davide Delugas]

Hello

It’s hard to say what went wrong without inspecting the log files.
It seems that autoconf wasn’t able to compile the test program; usually it 
happens because the shared libraries are not in
the LD_LIBRARY_PATH. But this is not your case

You should check what compilers are set in the make.inc file ( the lines with 
F90= … , MPIF90= … ) these are the compiler that devxlig config tries to use.

You can also try to compile the program using the CMake build system (see 
here)   it is 
unusual that they both fail…
Hope it helps
Kind regards – Pietro
Sent from Mail for Windows

From: inagaki ctec
Sent: Thursday, September 23, 2021 4:28 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] qe-6.8 with CUDA compiling unsuccessfully

Dear experts.

I am trying to compile qe-6.8 with CUDA.
But stacked at make which said to me,

~~~
checking whether we are cross compiling... configure: error: in 
`/home/jun/codes/qe-6.8/external/devxlib':
configure: error: cannot run Fortran compiled programs.
~~~

Information:

When echo,
$ echo $LD_LIBRARY_PATH
/opt/nvidia/hpc_sdk/Linux_x86_64/21.9/comm_libs/mpi/lib/:/opt/nvidia/hpc_sdk/Linux_x86_64/2021/compilers/lib/:/opt/nvidia/hpc_sdk/Linux_x86_64/21.9/REDIST/compilers/lib/:

configuration is:
F77=pgf77 F90=pgf90 MPIF90=pgf90 ./configure --prefix=/home/jun/codes/qe-6.8 
--with-cuda=yes --with-cuda-runtime=11.4 --with-cuda-cc=70 --disable-parallel

and resulted in:

ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...).  This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.

The following libraries have been found:
  BLAS_LIBS=-lblas
  LAPACK_LIBS=-L/opt/nvidia/hpc_sdk/Linux_x86_64/21.9/REDIST/compilers/lib/ 
-llapack -lblas
  FFT_LIBS= -lfftw3



Please check if this is what you expect.

If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
  ./configure LIBDIRS="list of directories, separated by spaces"

Configured for compilation of serial executables.

For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).

configure: success

Over.
Thank you.
--
Best Regards,
Jun Inagaki(稻垣 淳)
Mobile: (886)918002860
Department of Physics, Tamkang University, Taiwan.

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Re: [QE-users] [QE-GPU] - Error 'making' pw

[Pietro Davide Delugas]

Hi
You need to edit the make.inc file and recompile.
It the line with
CUDA_LIBS=-cudalib=cufft,cublas,cusolver   … etc

You need to add curan

Like this

CUDA_LIBS=-cudalib=cufft,cublas,cusolver,curand

Kind regards
Pietro

Sent from Mail for Windows

From: Anson Thomas
Sent: Thursday, September 23, 2021 5:09 AM
To: users@lists.quantum-espresso.org
Subject: [QE-users] [QE-GPU] - Error 'making' pw

I am trying to install the latest version of quantum espresso (6.8) with GPU- 
support on an Ubuntu 18.04.5 LTS (GNU/Linux 4.15.0-135-generic x86_64)

System Configuration:
Processor: Intel Xeon Gold 5120 CPU ],[ 2.20 GHz (2 Processor)
RAM: 96 GB
HDD: 6 TB
Graphics Card: NVIDIA Quadro P5000 (16 GB)

Following the steps given at https://gitlab.com/QEF/q-e-gpu/-/wikis/home, I 
installed all required packages (CUDA Toolkit v8+, PGI Compilers v17.10+, 
OpenMP package v3+), and tried configuring using

./configure --with-cuda="/opt/nvidia/hpc_sdk/Linux_x86_64/21.7/cuda/11.4/" 
--with-cuda-runtime=11.4 --with-cuda-cc=6.1 --enable-openmp --with- scalapack=no

It successfully configures, but on doing 'make all',

It works fine until it starts compiling pw.x. This is the error that I am 
getting

make[1]: Entering directory '/home/anson/qe/qe-6.8/PW'
( cd src ; make all || exit 1 )
make[2]: Entering directory '/home/anson/qe/qe-6.8/PW/src'
if test -n "" ; then \
( cd ../.. ; make  || exit 1 ) ; fi
mpif90 -mp -cuda -gpu=cc6.1,cuda11.4 -o pw.x \
   pwscf.o  libpw.a ../../Modules/libqemod.a ../../KS_Solvers/libks_solvers.a 
../../upflib/libupf.a ../../XClib/xc_lib.a ../../FFTXlib/libqefft.a 
../../LAXlib/libqela.a ../../UtilXlib/libutil.a ../../dft-d3/libdftd3qe.a 
/home/anson/qe/qe-6.8//clib/clib.a /home/anson/qe/qe-6.8//MBD/libmbd.a  
-cudalib=cufft,cublas,cusolver 
/home/anson/qe/qe-6.8//external/devxlib/src/libdevXlib.a 
/home/anson/qe/qe-6.8//EIGENSOLVER_GPU/lib_eigsolve/lib_eigsolve.a 
-L/home/anson/qe/qe-6.8//external/devxlib/src -ldevXlib  -L/usr/local/lib 
-llapack  -lblas  -L/home/anson/qe/qe-6.8//FoX/lib  -lFoX_dom -lFoX_sax 
-lFoX_wxml -lFoX_common -lFoX_utils -lFoX_fsys   -lblas
../../Modules/libqemod.a(random_numbers_gpu.o): In function 
`random_numbers_gpum_randy_vect_gpu_':
/home/anson/qe/qe-6.8/Modules/random_numbers_gpu.f90:67: undefined reference to 
`curandDestroyGenerator'
/home/anson/qe/qe-6.8/Modules/random_numbers_gpu.f90:68: undefined reference to 
`curandCreateGenerator'
/home/anson/qe/qe-6.8/Modules/random_numbers_gpu.f90:69: undefined reference to 
`curandSetPseudoRandomGeneratorSeed'
/home/anson/qe/qe-6.8/Modules/random_numbers_gpu.f90:73: undefined reference to 
`curandGenerateUniformDouble'
pgacclnk: child process exit status 1: /usr/bin/ld
Makefile:315: recipe for target 'pw.x' failed
make[2]: *** [pw.x] Error 2
make[2]: Leaving directory '/home/anson/qe/qe-6.8/PW/src'
Makefile:9: recipe for target 'pw' failed
make[1]: *** [pw] Error 1
make[1]: Leaving directory '/home/anson/qe/qe-6.8/PW'
Makefile:70: recipe for target 'pw' failed
make: *** [pw] Error 1



Any suggestions to solve this would be greatly appreciated.

Thank you.

--
Sent by ANSON THOMAS
IIT Roorkee, India

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Re: [QE-users] Effective Mass Tensor unit-cell dependency

[Pietro Davide Delugas]

Sorry probably  I am misunderstanding you question.
Are you taking into account the  band folding when you compute the mass tensor 
in the cubic supercell ?
If I have understood well what you are doing, you should compare the 
conduction-band’s  effective masses at Gamma in the cubic  supercell with those 
at X in the fcc cell at X.

[Silicon - The Yambo Project]

Regards – Pietro


Sent from Mail for Windows

From: Schön, Carl-Friedrich
Sent: Tuesday, September 21, 2021 11:47 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Effective Mass Tensor unit-cell dependency

Dear Paolo,

I take no responsibility to which unit cell is called what, I can never 
remember... Maybe my mind is too primitive to recognize the correct convention 
;-)

I tried using ibrav=2 etc. for the 2-atom UC, but the results were (almost) 
identical to the ibrav=0 2-atom UC input:

(Tensor for ibrav=2)
0.882  , 0.0, 0.0
0.0, 0.294  , -1.47
0.0, -1.47  , 2.352

(Slight difference as I used a slightly different lattice parameter, but the 
shape of the tensor is identical)

Hence not the one I would expect and see in the 8-atom UC. The reason I am 
using ibrav=0 is simply due to the way I generate my input files. As far as I 
understood it, it should not make a difference for the calculation, right?

Thanks and all the best,

Carl-Friedrich




Am 21.09.2021 um 15:49 schrieb Paolo Giannozzi 
mailto:p.gianno...@gmail.com>>:

Funny: I have always called "primitive" the 2-atom cell. "conventional" the 
8-atom one. Anyway, the 2-atom diamond structure (fcc lattice) is simply
  ibrav=2, a=lattice parameter (A)
or
  ibrav=2, celldm(1)=lattice parameter (a.u.)
(lattice parameter=side of the cube) plus
ATOMIC_POSITIONS (alat)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
or
ATOMIC_POSITIONS (crystal)
Si 0.00 0.00 0.00
Si 0.25 0.25 0.25
or any of the various possible ways of specifying atomic positions. If you do 
things properly you will find that the 2-atom and 8-atom cells give exactly the 
same results.

Paolo

On Mon, Sep 20, 2021 at 1:28 PM Schön, Carl-Friedrich 
mailto:sch...@physik.rwth-aachen.de>> wrote:
Dear QE users,

I have a question regarding the effective mass tensor, that I cannot seem to 
find the solution for. One could also rephrase this as a general question 
regarding the energy eigenvalues of k-points within different representations 
of unit-cells.
I have used QE to calculate the bands/eigenvalues of Silicon. I have done this 
ones with the conventional unit cell (from materials project):

Si2
1.0
3.8681383004362986 0.0 0.0
1.9340686210409386 3.349905532609194 0.0
1.9340686210409386 1.1166353539288019 3.1583211568194507
Si
2
Direct
0.25000 0.25000 0.25000
0.0 0.0 0.0


As well as the primitive unitcell:
Si8
1.0
5.4687280655 0.00 0.00
0.00 5.4687280655 0.00
0.00 0.00 5.4687280655
Si
8
Direct
0.25000 0.75044 0.25000
-0.0 -0.0 0.5
0.25000 0.25000 0.75044
-0.0 0.5 0.0
0.75044 0.75044 0.75044
0.5 0.0 0.0
0.75044 0.25000 0.25000
0.5 0.5 0.5


Let's look at the gamma point only at this point: I then constructed (using the 
emc.py script) a cartesian k-point grid around the Gamma point in order to get 
the effective mass tensor for the gamma point for each definition of the unit 
cell (Conduction Band). For the primitive, 8 atom unit cell, I get something 
like:

-20.46496343 0. 0.
0. -20.46496343 0.
0. 0. -20.46496343

with all Eigenvalues being -20.465 (the tensors are given in units of 1/m*). As 
far as I am aware, this is what it should look like in terms of 
symmetry/degeneracy (the absolute values are not of interest at this point).

If I look at the conventional, 2 atom unit cell, I get something like:
0.88345374 -0.00018375 -0.00018375
-0.00018375 0.11245293 -1.46684926
-0.00018375 -1.46684926 2.17115005
with non-degenerate eigenvalues of -0.65, 0.88, 2.93.
I do not understand how this can be. I would understand that the tensors might 
look different due to different (absolute) orientation in k-space, but the 
eigenvalues should remain identical, should they not? Otherwise the physics 
would have changed. Especially in the example of the Gamma point above, I would 
have assumed to get the exact same tensor, as the effective masses are equal in 
all directions. Again, the dense grid around the Gamma point is constructed as 
cartesian cube in both cases.

I therefore looked at the eigenvalues (energies in the conduction band) of the 
nscf calculation of said dense grid:
Points that should be equivalent (and are indeed identical in the primitive 8 
atom case) are not in the 2 atom case, e.g. E(0.01,0,0)!=E(0,0.01,0). I 

Re: [QE-users] QE6.8 ESM updated manual?

[Pietro Davide Delugas]

Thanks for reporting the issue and sorry for the incovenience.
I am doing the update of the manuals. The html one should be already up 
to date.

Pietro

On 8/31/21 4:39 AM, Hong Tang wrote:

Dear QE masters:

It looks that the QE website of the PW.x input description is not 
updated to the newest QE6.8.
For example, I tried and found that the keyword " lfcpopt " is not 
allowed in QE6.8.
Could you please let us know where we can check the new input 
description for QE6.8?


I thank you very much.

Best,
Hong


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Re: [QE-users] How to extract the px, py, pz, dz2, ....contributions with SOC from projdos out

[Pietro Davide Delugas]

P.S. the trick works easily only in the case that the relativistic 
pseudo-potential is norm-conserving.


On 7/5/21 12:13 PM, Pietro Davide Delugas wrote:

Dear Elie
keeping in mind the caveat of Thomas you could  in fact "cheat" 
projwfc in projecting your eigenstates into the non-relatistic atomic 
states labeled with l and the spin (up or down along z).
You just have to open the xml restart file ( the one inside  the 
prefix.save directory) look for the output element and, inside it,  
the magnetization element,

there change the  element from true to false.

hope this helps
Pietro





On 7/4/21 8:37 PM, Elio Physics wrote:

Dear Thomas,

Thank you for the generous and detailed answer. Indeed, what made me 
confused is that some papers still use the terminology "dz2' ,for 
example, even in the presence of the SOC. I will definitely be 
looking at the papers you suggested to decide which option I will 
adopt for the discussion I need.


Regards


*From:* Thomas Brumme 
*Sent:* Sunday, July 4, 2021 10:24 AM
*To:* Quantum ESPRESSO users Forum 
; Elio Physics 
*Subject:* Re: [QE-users] How to extract the px, py, pz, dz2, 
contributions with SOC from projdos out


Dear Elie,


The short answer is: You can't!


Spin-orbit interaction couples the orbital angular momentum with the 
spin momentum and thus neither l or s are good quantum number 
anymore. You now have to use the total angular momentum J. Sure, a 
lot of people still use the nomenclature from the non-SOC 
calculations, such as speaking in the case of 2D TMDCs of dz² states 
at the K point, but strictly speaking this is not correct. If you 
really want to understand the relation between J and L in detail, I 
can recommend the paper by Andrea Dal Corso and Adriano Mosca Conte, 
Phys. Rev. B 71, 115106 (2005) 
(https://link.aps.org/doi/10.1103/PhysRevB.71.115106 
<https://link.aps.org/doi/10.1103/PhysRevB.71.115106>) which nicely 
shows which spherical harmonics are included in which spin-angle 
functions for which total angular momentum j. If I remember this 
correctly (some time ago that I did this and I can't find the table 
anymore) the states with higher mj (+-3/2 and +- 5/2) have more 
in-plane characterfor both j=3/5 and j=5/2 (i.e., the contain terms 
with spherical harmonics which are usually combined such that the 
result is in the xy-plane) while the states with mj=+-1/2 have more 
out-of-plane character (z direction). But I could be wrong here since 
I don't have the details anymore.



The only option for you - if you don't want to check the paper or if 
this is too much and if nobody else comments here - is to do a 
non-SOC calculation and then hope that SOC is not mixing states too 
much and you can still call the result, e.g., dz² like. OR you plot 
the corresponding wave function in real space and decide by "looking" 
at the form of |psi|².



Regards


Thomas



P.S.: another detail concerning, e.g., the states at K in a WS2 
monolayer - is this your system? :)


The states are not simple split into spin up and spin down even if a 
lot of people use this nomenclature. For the valence band the two 
SOC-split bands are to nearly 100% spin up or down but not for the 
conduction band where you won't have states which are 100% up or 
down, even if there is no in-plane contribution... Some details can 
also be found here: 
https://link.aps.org/doi/10.1103/PhysRevB.101.235408 
<https://link.aps.org/doi/10.1103/PhysRevB.101.235408>



On 7/4/21 6:52 AM, Elio Physics wrote:

Dear all,

I am studying the contribution of the orbitals to the bands of a 
structure, in the presence of spin orbit coupling. At the beginning 
of the projwfc.x output file, I got:


 state #   1: atom   1 (S  ), wfc  1 (l=0 j=0.5 m_j=-0.5)
     state #   2: atom   1 (S  ), wfc  1 (l=0 j=0.5 m_j= 0.5)
     state #   3: atom   1 (S  ), wfc  2 (l=1 j=0.5 m_j=-0.5)
     state #   4: atom   1 (S  ), wfc  2 (l=1 j=0.5 m_j= 0.5)
     state #   5: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j=-1.5)
     state #   6: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j=-0.5)
     state #   7: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j= 0.5)
     state #   8: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j= 1.5)
.
.
.
  state #  39: atom   5 (W ), wfc  3 (l=2 j=1.5 m_j=-1.5)
     state #  40: atom   5 (W), wfc  3 (l=2 j=1.5 m_j=-0.5)
     state #  41: atom   5 (W), wfc  3 (l=2 j=1.5 m_j= 0.5)
     state #  42: atom   5 (W), wfc  3 (l=2 j=1.5 m_j= 1.5)
     state #  43: atom   5 (W ), wfc  4 (l=2 j=2.5 m_j=-2.5)
     state #  44: atom   5 (W ), wfc  4 (l=2 j=2.5 m_j=-1.5)
     state #  45: atom   5 (W), wfc  4 (l=2 j=2.5 m_j=-0.5)
     state #  46: atom   5 (W), wfc  4 (l=2 j=2.5 m_j= 0.5)
     state #  47: atom   5 (W), wfc  4 (l=2 j=2.5 m_j= 1.5)

The l=1 wavefunctions are the p contributions. But How can we 
specifically identify which one is px, py and pz?
Simi

Re: [QE-users] How to extract the px, py, pz, dz2, ....contributions with SOC from projdos out

[Pietro Davide Delugas]

Dear Elie
keeping in mind the caveat of Thomas you could  in fact "cheat" projwfc 
in projecting your eigenstates into the non-relatistic atomic states 
labeled with l and the spin (up or down along z).
You just have to open the xml restart file ( the one inside  the 
prefix.save directory) look for the output element and, inside it,  the 
magnetization element,

there change the  element from true to false.

hope this helps
Pietro





On 7/4/21 8:37 PM, Elio Physics wrote:

Dear Thomas,

Thank you for the generous and detailed answer. Indeed, what made me 
confused is that some papers still use the terminology "dz2' ,for 
example, even in the presence of the SOC. I will definitely be looking 
at the papers you suggested to decide which option I will adopt for 
the discussion I need.


Regards


*From:* Thomas Brumme 
*Sent:* Sunday, July 4, 2021 10:24 AM
*To:* Quantum ESPRESSO users Forum ; 
Elio Physics 
*Subject:* Re: [QE-users] How to extract the px, py, pz, dz2, 
contributions with SOC from projdos out


Dear Elie,


The short answer is: You can't!


Spin-orbit interaction couples the orbital angular momentum with the 
spin momentum and thus neither l or s are good quantum number anymore. 
You now have to use the total angular momentum J. Sure, a lot of 
people still use the nomenclature from the non-SOC calculations, such 
as speaking in the case of 2D TMDCs of dz² states at the K point, but 
strictly speaking this is not correct. If you really want to 
understand the relation between J and L in detail, I can recommend the 
paper by Andrea Dal Corso and Adriano Mosca Conte, Phys. Rev. B 71, 
115106 (2005) (https://link.aps.org/doi/10.1103/PhysRevB.71.115106 
) which nicely 
shows which spherical harmonics are included in which spin-angle 
functions for which total angular momentum j. If I remember this 
correctly (some time ago that I did this and I can't find the table 
anymore) the states with higher mj (+-3/2 and +- 5/2) have more 
in-plane characterfor both j=3/5 and j=5/2 (i.e., the contain terms 
with spherical harmonics which are usually combined such that the 
result is in the xy-plane) while the states with mj=+-1/2 have more 
out-of-plane character (z direction). But I could be wrong here since 
I don't have the details anymore.



The only option for you - if you don't want to check the paper or if 
this is too much and if nobody else comments here - is to do a non-SOC 
calculation and then hope that SOC is not mixing states too much and 
you can still call the result, e.g., dz² like. OR you plot the 
corresponding wave function in real space and decide by "looking" at 
the form of |psi|².



Regards


Thomas



P.S.: another detail concerning, e.g., the states at K in a WS2 
monolayer - is this your system? :)


The states are not simple split into spin up and spin down even if a 
lot of people use this nomenclature. For the valence band the two 
SOC-split bands are to nearly 100% spin up or down but not for the 
conduction band where you won't have states which are 100% up or down, 
even if there is no in-plane contribution... Some details can also be 
found here: https://link.aps.org/doi/10.1103/PhysRevB.101.235408 




On 7/4/21 6:52 AM, Elio Physics wrote:

Dear all,

I am studying the contribution of the orbitals to the bands of a 
structure, in the presence of spin orbit coupling. At the beginning 
of the projwfc.x output file, I got:


 state #   1: atom   1 (S  ), wfc  1 (l=0 j=0.5 m_j=-0.5)
     state #   2: atom   1 (S  ), wfc  1 (l=0 j=0.5 m_j= 0.5)
     state #   3: atom   1 (S  ), wfc  2 (l=1 j=0.5 m_j=-0.5)
     state #   4: atom   1 (S  ), wfc  2 (l=1 j=0.5 m_j= 0.5)
     state #   5: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j=-1.5)
     state #   6: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j=-0.5)
     state #   7: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j= 0.5)
     state #   8: atom   1 (S  ), wfc  3 (l=1 j=1.5 m_j= 1.5)
.
.
.
  state #  39: atom   5 (W ), wfc  3 (l=2 j=1.5 m_j=-1.5)
     state #  40: atom   5 (W), wfc  3 (l=2 j=1.5 m_j=-0.5)
     state #  41: atom   5 (W), wfc  3 (l=2 j=1.5 m_j= 0.5)
     state #  42: atom   5 (W), wfc  3 (l=2 j=1.5 m_j= 1.5)
     state #  43: atom   5 (W ), wfc  4 (l=2 j=2.5 m_j=-2.5)
     state #  44: atom   5 (W ), wfc  4 (l=2 j=2.5 m_j=-1.5)
     state #  45: atom   5 (W), wfc  4 (l=2 j=2.5 m_j=-0.5)
     state #  46: atom   5 (W), wfc  4 (l=2 j=2.5 m_j= 0.5)
     state #  47: atom   5 (W), wfc  4 (l=2 j=2.5 m_j= 1.5)

The l=1 wavefunctions are the p contributions. But How can we 
specifically identify which one is px, py and pz?
Similary, how to identify which ones of the 10 d orbitals are the 
dz^2 for example


regards

Elie
Federal Universiy of Rondonia
Brazil

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Re: [QE-users] Relaxation of W2N Error

[Pietro Davide Delugas]

your cutoff (25 Ry) is quite low, you will likely want  to increase it 
and  in this case the problem could disappear.


If you want to use this cutoff with the same number of MPI tasks, you 
could instead  use more pools,

use the command option -nk
e.g.

pw.x -nk 2
or
pw.x -nk 4

Pietro

On 7/2/21 5:44 PM, Rutika Savaliya wrote:

Thank You for the response.
Can I know how can I tackle this issue

Rutika Savaliya

*From:* users  on behalf of 
Paolo Giannozzi 

*Sent:* Friday, July 2, 2021 10:56:36 AM
*To:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] Relaxation of W2N Error
On Fri, Jul 2, 2021 at 4:45 PM Rutika Savaliya 
> wrote:


     Parallel version (MPI), running on   192 processors

     Error in routine n_plane_waves (1):
     No plane waves found: running on too many processors?


The answer is "yes, running on too many processors"

Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222


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Re: [QE-users] Getting wavefunctions from QE

[Pietro Davide Delugas]

Hi Andrew

one easy way to get the wavefunctions in text format --but are you 
really sure that you want to do it ?-- is to compile pw 
 
with the support for hdf5  , there will be and hdf5 file for each 
k-point, and you can convert them to text format  format using the  
h5dump program.


h5dum -d evc prefix.hdf5

it will printout a 2 dimensional dataset ( the first index C convention 
in the band index, the other one is the plane wave index)

I hope it helps
Pietro

On 9/17/20 8:31 AM, Andrew Xu wrote:

Dear users,

I'm trying to extract the wavefunctions in QE after running pw.x, 
preferably in non-binary format. In versions less than 6, these two 
links give me what I want 
(https://pw-forum.pwscf.narkive.com/UnDfSmzu/how-to-use-the-wave-functions, 
https://lists.quantum-espresso.org/pipermail/users/2011-June/020897.html); 
how can I do a similar thing for QE version 6?


In particular (I'm using QE 6.3), I noticed the QExml_example in 
~espresso/PP/ is missing in QE version 6, and when I do make qexml.x 
in ~espresso/PP/, I get errors. There's a qexml.f90 in Modules, but 
doing make qexml.f90, make qexml.o, make qexml_module.mod don't do 
anything.


Best,
Andy

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Re: [QE-users] Pseudo potential

[Pietro Davide Delugas]

P.S.

Andrea dal Corso just made me notice that to study the magnetism you   
need an Nd  pseudo with 4F in valence.

Which was actually, maybe your first question.

at the link below you may dowload the one from the pseudolibrary.


https://filesender.garr.it/?s=download&token=a22f441c-9e68-4bba-8bf8-a5c8c8cf9efe
regards Pietro

On 8/31/20 10:17 AM, Pietro Delugas wrote:


Hi

 from the results of your calculation you have fractional 
occupations.  Does the literature report this material as insulator or 
as metal ?


 It might be that this fractional occupations are caused by the wrong 
dispersion of the some atomic states. This a very well known problem 
of LDA or PBE with localized d or f atomic states. One way to correct 
this behavior is using LDA+U approach.


I hope this helps

regards

Pietro

On 31/08/20 09:46, tanmay chaki wrote:

Dear sir,
As your suggestions I have changed the required things. But I got 
total magnetization zero. but this compound has a magnetic moment 
which is reported in the journal. I have attached the input and 
output file. please help me to do correct calculations.

Thanking you.

Tanmay Chaki
Research Scholar
N.B.U


On Fri, Aug 28, 2020 at 11:16 PM tanmay chaki > wrote:


Thanks for your suggestions

On Fri, 28 Aug, 2020, 10:43 pm Yuvam Bhateja, mailto:yuvam...@gmail.com>> wrote:

Hey,

As per my knowledge, there's no specific pseudopotential for
spin calculation.

You need to use commands like nspin and
starting_magnetization in order to start your spin calculation.

Your choice of XC Functional can affect the results in your
spin calculation.

Let me know if it helps.

Regards
Yuvam Bhateja

On Fri, 28 Aug 2020, 10:38 pm tanmay chaki,
mailto:tanmaych...@gmail.com>> wrote:

Hello QE users,
Is there any specific Pseudo potential for spin polarized
calculation?
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Re: [QE-users] Wrong electron number in superposition of atomic charge densities

[Pietro Davide Delugas]

Ciao Nicola

Quick and I don't know how dirty: generate a pseudo with 12 electrons   
copy  the rhoatom section from there  and copy it in  place of the 11 
electrons rhoat in the pseudo you've been using.

 greetings - Pietro


On 8/27/20 5:28 PM, Colonna Nicola (PSI) wrote:


Dear QE experts,


 I recently perfomed a scf PBEsol calculation for Tb2Ti2O7 (attached 
the input file).


 I would like to plot the difference between the scf charge density 
and the superposition


 of atomic charge. For this purpose I used the PostProcessing tool 
(plut_num = 9).



 I expected the integral of this difference to be ~0 , but I found it 
to be 4. After a quick check


 I realized that the Ti pseudopotetial (GBRV-1.4, 
ti_pbesol_v1.4.uspp.F.UPF) was generated


 in an ionized configuration with just 1 electron (instead of 2 ) in 
the  3d orbital. Since there


 are 4 Ti in the primitive cell, I think this is the reason for the 
odd result described above.



 Indeed during the initialization of a scf calculation for an isolated 
Ti atom I got:


Initial potential from superposition of free atoms
 Check: negative starting charge=   -0.001319
 starting charge   10.6, renormalised to   12.0

 However this renormalization is not done in the PP, and in any case I 
do not think it would make sense there.



 That said, my feeling is that I cannot completely trust the charge 
density difference.


 Do you have any advise on how to solve this problem (beside changing 
pseudo)?



 Thank you in advance and best regards,


Nicola Colonna



-
PAUL SCHERRER INSTITUT
Nicola S. Colonna
WHGA/150
CH-5232 Villigen-PSI

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Re: [QE-users] ?= ?= Same run not accelerated when starting from converged rho and w

[Pietro Davide Delugas]

sorry  I missed your answer.

maybe we are missing to load  the paw part of the density. It is still 
written in a file apart.


we should open an issue on gitlab, otherwise we will forget about it again

Pietro

On 8/18/20 10:45 AM, Antoine Jay wrote:

Dear Pietro,
This happens always not only in library mode.
This does not happen with US pseudo.
In attached files: 1rst step and 2nd step with us and paw (and a paw 
with high diago accuracy for stephano).

The 2nd step is a relax so you can see that the sequence
    "Initial potential from superposition of free atoms
    + "a scf correction to at. rho is read from "rho.in"   (rho.in is 
obtained from output_drho of the 1rst job so it's scf-at.pot)

    + "Starting wfcs from file"
is not equivalent (in the PAW case) to the potential extrapolation
" NEW-OLD atomic charge density approx. for the potential"

Regards,

Antoine Jay
LAAS-CNRS
Toulouse, France


Le Lundi, Août 17, 2020 09:36 CEST, Pietro Delugas  
a écrit:


Hi

It’s strange.  Have you checked whether this happens only in library 
mode or always ? What about if you use uspp instead of paw ?


Sent from Mail  for 
Windows 10


*From: *Antoine Jay 
*Sent: *Monday, August 17, 2020 9:16 AM
*To: *Quantum ESPRESSO users Forum 

*Subject: *Re: [QE-users]?==?utf-8?q? ?==?utf-8?q? ?= Same run not 
accelerated when starting from converged rho and wf


Dear Stephano,
I reduced diago_thr_init to 1.0D-13 but it changed nothing to the 
first estimated scf accuracy.:


   Initial potential from superposition of free atoms
 a scf correction to at. rho is read 
from./calcforces_QE/step/initialization/initial_bassin/relax//results/dbed.relax.save/rho.in

 negative rho (up, down):  1.432E-02 0.000E+00
 Starting wfcs from file
 Checking if some PAW data can be deallocated...
   PAW data deallocated on    4 nodes for type:  1
   PAW data deallocated on   32 nodes for type:  2
   PAW data deallocated on   35 nodes for type:  3
 total cpu time spent up to now is   29.8 secs
 Self-consistent Calculation
 iteration #  1 ecut=    58.00 Ry beta= 0.10
 Davidson diagonalization with overlap
 c_bands:  5 eigenvalues not converged
 ethr =  1.00E-13,  avg # of iterations = 40.0
 negative rho (up, down):  1.432E-02 0.000E+00
 total cpu time spent up to now is  813.3 secs
 total energy  =  -11390.75602693 Ry
 Harris-Foulkes estimate   =  -11390.75013390 Ry
 estimated scf accuracy    <   0.00021610 Ry
 iteration #  2 ecut=    58.00 Ry beta= 0.10
 Davidson diagonalization with overlap
 ethr =  2.16E-08,  avg # of iterations =  1.0
... and the rest of the file is the same as the qe.0002.out I send.

Please note that I start from the wfcs of exactely the same 
configuration and parameters by using startingwfc='file',

but I do not use startingpot='file'.
Instead I have activated input_drho='rho.in'
This 'rho.in' file is a copy of the file 'rho.out' that have been 
created by activating the parameter input_drho='rho.out'.
This trick is done because sometimes, the atomic positions have a 
small variation (but not in this case).


Please note that I already tried this trick on smaller systems plenty 
of times and I never saw this problem,
this is why I wonder if it is a problem of the system size or of the 
PAW pseudo for wich for example the becsum couldbe bad performed when 
some PAW data are deallocated:

" Checking if some PAW data can be deallocated...
   PAW data deallocated on    4 nodes for type:  1
   PAW data deallocated on   32 nodes for type:  2
   PAW data deallocated on   35 nodes for type:  3"


Regards,

Antoine Jay
LAAS-CNRS
Toulouse, France








Le Dimanche, Août 16, 2020 23:20 CEST, Stefano de Gironcoli 
 a écrit:


6.d-9 is still too large.. it should be something like 1d-13 to aim at 
a smaller scf estimate.


are you really starting from the scf charge and wfcs of the same 
conficuration ?


stefano

On 16/08/20 22:05, Antoine Jay wrote:

Dear Stephano,
adding diago_thr_int=1.0D-8 does not change the first conv_thr
(exept the average#of iterations)
As you said, the first value 1.0D-2 is detected to  be too large
and is updated to 6.0D-9 so I don't see why changing manually the
first value would change something if it is already automatically
changed...

Antoine Jay
LAAS-CNRS
Toulouse, France

Le Samedi, Août 15, 2020 17:10 CEST, Stefano de Gironcoli
  a écrit:

Hi Antoine,

  don't know exactly why you get this result but one thing you can
try is to set diag_thr_init ~ conv_thr/Nelec/10 so the first
diagonalization is pushed tighter (if the wfcs are already very
good it should not take too many iterations) and the computed dr2
estimate should be more faithful

  

Re: [QE-users] Error in installing thermo_pw 1.2.1 with QE-6.5

[Pietro Davide Delugas]

sorry but isn't this

https://www.mail-archive.com/users@lists.quantum-espresso.org/msg38069.html

an answer to the same question posted by  you ?
If the case the answer didn't work would be more useful to continue with 
the same thread.


Pietro

On 8/20/20 9:58 AM, Pooja Vyas wrote:
While I try to install thermo_pw, on giving the command "make 
thermo_pw", I get following error,


test -d bin || mkdir bin
( cd clib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/clib'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/clib'
cd install ; make -f extlibs_makefile libiotk
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/install'
if test ! -d ../S3DE; then \
(gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \
if test -e Makefile_iotk; then \
        (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \
if test -e iotk_config.h; then \
(cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi
cd ../S3DE/iotk/src; make lib+util;
make[2]: Entering directory '/home/pooja/q-e-qe-6.5/S3DE/iotk/src'
make[2]: Nothing to be done for 'lib+util'.
make[2]: Leaving directory '/home/pooja/q-e-qe-6.5/S3DE/iotk/src'
cd ../bin; ln -fs ../S3DE/iotk/tools/iotk .; \
ln -fs ../S3DE/iotk/src/iotk.x .; \
ln -fs ../S3DE/iotk/src/iotk_print_kinds.x .; \
# middle instruction needed for windows
cd ../; rm -rf iotk ; ln -fs S3DE/iotk iotk
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/install'
cd install ; make -f extlibs_makefile libfox
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/install'
echo

if test ! -d ../FoX; then \
        mkdir ../FoX; \
(gzip -dc ../archive/fox.tgz | (cd ../FoX; tar -xvf -)); \
cd ../FoX/fox/; export FC=gfortran; export FCFLAGS=""; \
./configure --prefix=/home/pooja/q-e-qe-6.5//FoX ;\
make install; cd ../; rm -fr fox;fi
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/install'
( cd UtilXlib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/UtilXlib'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/UtilXlib'
cd install ; make -f extlibs_makefile liblapack
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/install'
if test ! -e ../LAPACK; then (gzip -dc ../archive/`echo 
"http://www.netlib.org/lapack/lapack-3.6.1.tgz"; | sed 
's/.*\///;s/.*=//'` | (cd ../ ; tar -xvf - ) ) ; if test "`echo $?`" 
-ne "0" ; then echo "*** Unable to download 
http://www.netlib.org/lapack/lapack-3.6.1.tgz."; ; echo "*** Verify 
that the url is correct." ; exit 1 ; else (cd ../ ; ln -s lapack-3.6.1 
LAPACK) ; fi ; fi

if test ! -e ../LAPACK/liblapack.a && test -e make_lapack.inc; then \
  (cp make_lapack.inc ../LAPACK/make.inc; \
  cd ../LAPACK; make blaslib lapacklib); else \
        (echo "no configuration file found for lapack"; \
         echo "run configure from main QE dir"; exit); fi
no configuration file found for lapack
run configure from main QE dir
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/install'
cd install ; make -f extlibs_makefile libcuda
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/install'
make[1]: Nothing to be done for 'libcuda'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/install'
( cd LAXlib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/LAXlib'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/LAXlib'
( cd FFTXlib ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/FFTXlib'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/FFTXlib'
( cd Modules ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/Modules'
make[1]: Nothing to be done for 'all'.
make[1]: Leaving directory '/home/pooja/q-e-qe-6.5/Modules'
( cd KS_Solvers ; make TLDEPS= all || exit 1 )
make[1]: Entering directory '/home/pooja/q-e-qe-6.5/KS_Solvers'
if test -d Davidson_RCI ; then \
( cd Davidson_RCI ; make all || exit 1 ) ; fi
make[2]: Entering directory 
'/home/pooja/q-e-qe-6.5/KS_Solvers/Davidson_RCI'

make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory 
'/home/pooja/q-e-qe-6.5/KS_Solvers/Davidson_RCI'

if test -d Davidson ; then \
        ( cd Davidson ; make all || exit 1 ) ; fi
make[2]: Entering directory '/home/pooja/q-e-qe-6.5/KS_Solvers/Davidson'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/pooja/q-e-qe-6.5/KS_Solvers/Davidson'
if test -d CG ; then \
        ( cd CG ; make all || exit 1 ) ; fi
make[2]: Entering directory '/home/pooja/q-e-qe-6.5/KS_Solvers/CG'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/pooja/q-e-qe-6.5/KS_Solvers/CG'
if test -d PPCG ; then \
        ( cd PPCG ; make all || exit 1 ) ; fi
make[2]: Entering directory '/home/pooja/q-e-qe-6.5/KS_Solvers/PPCG'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/home/pooja/q-e-qe-6.5/KS_Solvers/PPCG'
if test -d ParO 

Re: [QE-users] problem whem more than 1000 k-points

[Pietro Davide Delugas]

Hi

which version of the code are you using ? In the last version npk is 
already set to 4.



an easy solution could be to split the calculation in 2 or 3 independent 
calculations in which you compute a part of the k-points.
It might be a little be awkward to collect the results afterwards it 
depends, what you need them for.


Hope this helps - greetings Pietro

On 8/20/20 4:15 AM, Fanhao Jia wrote:

Dear developers,
I am doing a nscf calculation of GaAs with so many k-points.
I can run  the calculation if the number of k-points is 1000, and it 
is very fast to finish.
But when I increase to 12*12*12=1728 k-points, the  program does not 
really run, there is no output or error.
I have increased the nkp in Module/parameter.f90  to 10,  it 
doesn't help. Increasing cpus still doesn't help.

I have attached my input. If you have any idea, please let me know.
Best,
Fanhao

&control
   calculation = 'bands'
   pseudo_dir = '../'
/
&system
   ecutwfc = 60.0
   ibrav = 0
   nat = 2
   ntyp = 2
   nbnd=16
/
&electrons
   electron_maxstep = 100
   conv_thr = 1e-10
   diago_full_acc = .true.
   diago_david_ndim = 4
   mixing_ndim = 8
   mixing_mode = 'plain'
   diagonalization = 'david'
   mixing_beta = 0.7
/
CELL_PARAMETERS angstrom
   0.0 2.82675 2.82675
   2.82675 0.0 2.82675
   2.82675 2.82675 0.0
ATOMIC_SPECIES
   Ga 69.723 'Ga.UPF'
   As 74.9216 'As.UPF'
ATOMIC_POSITIONS crystal
   Ga 0.0 0.0 0.0
   As 0.25 0.25 0.25
K_POINTS crystal
  1728
  0.0   0.0  0.0  1.0
  0.0   0.0  0.08333  1.0
  0.0   0.0  0.16667  1.0
  0.0   0.0  0.25000  1.0
  0.0   0.0  0.3  1.0



贾帆豪
18329030...@163.com

 

签名由 网易邮箱大师  
定制


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

[Pietro Davide Delugas]

That's weird
I just checked the 6.5, the printout of atomic projected dos is there
have a look at matdyn.f90
at line 762 you should have

IF (ionode) WRITE (2, '(2ES18.10,1000ES12.4)') E, SUM(DOSofE(1:nat)), 
DOSofE(1:nat)




On 8/4/20 12:12 AM, Baer, Bradly wrote:
Actually, I just found this message in the mailing list archive.  I 
must have missed it due to poor word choice while searching originally.


https://lists.quantum-espresso.org/pipermail/users/2018-March/040476.html

It appears that this functionality was added in 2018, but I am unsure 
on how to check if this was something that was ever merged into the 
main distribution of QE(I am using 6.5) or if it is limited to the 
development branch or even only available through manual patching.  Is 
there some way for me to check or should I just attempt to apply the 
patch and see what happens?


-Brad


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



*From:* users  on behalf of 
Baer, Bradly 

*Sent:* Monday, August 3, 2020 4:49 PM
*To:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] Phonon Density of States by atomic type
Professor Marzari, I had generally followed the process of pw.x -> 
ph.x -> q2r.x ->Matdyn.x(dos)/matdyn.x(dispersion) -> plot.  I am 
assuming that is what you mean by interpolating to build the DOS 
myself?  Would you have any recommendations on resources/references to 
extend that process into obtaining the contributions from each atomic 
type?



To Pietro: I just went back and looked through some output files and I 
was unable to find the information you were referring to.  My .dos 
file only has two columns.  Below is both the input and output from 
the dos matdyn.x calculation. Perhaps I am doing something wrong?


_INPUT - GaNMatdyn.in_
 &input
    asr='simple',
    flfrc='GaN444.fc', dos=.true.
    fldos='phonon.dos', nk1=50, nk2=50, nk3=50
 /

_OUTPUT_
 -1.6359E+02  0.E+00
 -1.6259E+02  5.7394E-05
.
.
.
.
  6.9341E+02  1.6180E-05
  6.9441E+02  0.E+00



-Brad

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



*From:* Nicola Marzari 
*Sent:* Monday, August 3, 2020 1:03 PM
*To:* Quantum ESPRESSO users Forum ; 
Baer, Bradly 

*Subject:* Re: [QE-users] Phonon Density of States by atomic type
On 03/08/2020 18:39, Baer, Bradly wrote:
> Hello,
>
> I was consulting the reference materials on materialsproject.org
> 
> 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fwork%2Ftools%2Finteractivephonon&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=1T2HLQ694J5aEvZ%2FLgQP50VfjNfQ6qhsGa5QOZwfIL8%3D&reserved=0 


that allows you to explore graphically/interactively phonon dispersions
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fdiscover%2F2dstructures%2Fdetails%2FBN&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=Bgt18WK%2BonmwRVsgdpE3ciA6RnG

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

[Pietro Davide Delugas]

Hi Brad
Maybe you are using an old version. You will  find the atom projected 
phonon dos in any version released after February 2018.

Pietro

On 8/3/20 11:49 PM, Baer, Bradly wrote:
Professor Marzari, I had generally followed the process of pw.x -> 
ph.x -> q2r.x ->Matdyn.x(dos)/matdyn.x(dispersion) -> plot.  I am 
assuming that is what you mean by interpolating to build the DOS 
myself?  Would you have any recommendations on resources/references to 
extend that process into obtaining the contributions from each atomic 
type?



To Pietro: I just went back and looked through some output files and I 
was unable to find the information you were referring to. My .dos file 
only has two columns.  Below is both the input and output from the dos 
matdyn.x calculation. Perhaps I am doing something wrong?


_INPUT - GaNMatdyn.in_
 &input
    asr='simple',
    flfrc='GaN444.fc', dos=.true.
    fldos='phonon.dos', nk1=50, nk2=50, nk3=50
 /

_OUTPUT_
 -1.6359E+02  0.E+00
 -1.6259E+02  5.7394E-05
.
.
.
.
  6.9341E+02  1.6180E-05
  6.9441E+02  0.E+00



-Brad

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



*From:* Nicola Marzari 
*Sent:* Monday, August 3, 2020 1:03 PM
*To:* Quantum ESPRESSO users Forum ; 
Baer, Bradly 

*Subject:* Re: [QE-users] Phonon Density of States by atomic type
On 03/08/2020 18:39, Baer, Bradly wrote:
> Hello,
>
> I was consulting the reference materials on materialsproject.org
> 
 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://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fwork%2Ftools%2Finteractivephonon&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=1T2HLQ694J5aEvZ%2FLgQP50VfjNfQ6qhsGa5QOZwfIL8%3D&reserved=0
that allows you to explore graphically/interactively phonon dispersions
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.materialscloud.org%2Fdiscover%2F2dstructures%2Fdetails%2FBN&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=Bgt18WK%2BonmwRVsgdpE3ciA6RnG6W7F9z8KoDxyEBAM%3D&reserved=0

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
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX 
(https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2Fquantum-espresso&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344701373&sdata=Jt03%2Bj5ro6IG5HmpkwSHFewqTqwjbvevDrJ12BFWXQk%3D&reserved=0)

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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%7C7bea9744135d4f07c63808d837d794f5%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637320746344711366&sdata=69b6UN%2Bwxc8IsOtHrgcqaQNdClTXzhGhly1KV

Re: [QE-users] xml parser for data-file-schema.xml in qe

[Pietro Davide Delugas]

Hi Kumar

could you send me a snippet of the code you you used for parsing ?
You  can also post the issue directly in the issue of the repository. 
Disappointingly nobody has used that section yet


As a general answer parsing the xml file with python is very simple. You 
don't even need qeschema, the xmlschema package is sufficient, even if 
in that case you need to download the schema file by yourself, its 
location is printed in the header of the xml file.


For example if you
current url for example is

http://www.quantum-espresso.org/ns/qes/qes_190304.xsd

To convert the whole output of QE in a python dictionay the python lines 
are something like:


import xmlschema
from xml.etree import ElementTree

schema = xmlschema.XMLSCHEMA('qes_190304.xsd')
data = ElementTree.parse('prefix.save//data-file-schema.xml').getroot()
data_dict = schema.to_dict(data)




On 11/12/19 4:07 AM, Sonu Kumar wrote:

Dear QE users,

Is there any xml parser for data-file-schema.xml in "prefix".save 
directory of tmp directory?


I found qeschema (https://github.com/QEF/qeschema), but stuck by the 
attribute errors of the object XsdConstraintXPathParser 
(AttributeError: type object 'XsdConstraintXPathParser' has no 
attribute 'end')

Any suggestions for xml parser or the error would be appreciated.

best regards,
Kumar

**
*With kind regards,
*
*S Kumar |  PhD.
*
**

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Re: [QE-users] users Digest, Vol 148, Issue 3

[Pietro Davide Delugas]

Hi
the issue has been fixed in the developement version.
you can  download the the develop version of QE from gitlab

https://gitlab.com/QEF/q-e

or github.

https://github.com/QEF/q-e/tree/develop


hope it helps
best regards - Pietro

On 11/4/19 1:53 PM, Hussain Ali wrote:

subject: problem in cppp.x executable  

Dear QE Developers,

I am getting an error while post processing using cppp.x

  %%
      Error in routine  cppp (1):
       Cannot open file ./tmp//h2o_51.save/data-file.xml
  %%


Hussain
MS student
QAU, Islamabad Pakistan.

On Mon, Nov 4, 2019 at 4:01 PM 
> wrote:


Send users mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of users digest..."


Today's Topics:

   1. relation between Hubbard-U and core charge? (Malte Sachs)
   2. Re: DFT + U not working on Sn 4d (Ari P Seitsonen)
   3. Re: Error in interploation of IFCs by matdyn.x (Lorenzo
Paulatto)
   4. Plotting a 3D band plot using Quantum Espresso (Vasilios
Passias)
   5. Re: How to plot phonon band structure with LO-TO splitting
      (Lorenzo Paulatto)
   6. compiling GPU enabled version of QE:
      q-e-gpu-qe-gpu-6.4.1a1.tar.gz (Mohammad Moaddeli)
   7. Re: How to plot phonon band structure with LO-TO splitting
      (Dr. K. C. Bhamu)
   8. Re: How to plot phonon band structure with LO-TO splitting
      (Lorenzo Paulatto)
   9. Re: How to plot phonon band structure with LO-TO splitting
      (Dr. K. C. Bhamu)


--

Message: 1
Date: Sun, 3 Nov 2019 14:59:47 +0100
From: Malte Sachs mailto:malte.sa...@chemie.uni-marburg.de>>
To: Quantum Espresso users Forum mailto:users@lists.quantum-espresso.org>>
Subject: [QE-users] relation between Hubbard-U and core charge?
Message-ID:
       
mailto:e9fb07ea-4977-10e7-41aa-c7da74124...@chemie.uni-marburg.de>>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear DFT+U experts,

I am testing the hp.x code of the QE 6.4.1 version by calculating the
Hubbard-U of simple binary actinides compounds in a
"self-consistent"?
way. Within the same crystal structure and the same counter ions I
find
a perfect linear dependency of the U on the core charge Z of the
actinide ions. I am a little bit surprised about this result.
However, I
am not sure if this is surprising at all. I would thankful for any
help
or hints regarding this issue.

Best regards,

Malte Sachs

-- 
Malte Sachs

Anorganische Chemie, Fluorchemie
Philipps-Universit?t Marburg
Hans-Meerwein-Stra?e 4
35032 Marburg (Paketpost: 35043 Marburg)
Tel.: +49 (0)6421 28 - 25 68 0
http://www.uni-marburg.de/fb15/ag-kraus/


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--

Message: 2
Date: Sun, 3 Nov 2019 15:56:34 +0100 (CET)
From: Ari P Seitsonen mailto:ari.p.seitso...@iki.fi>>
To: Quantum ESPRESSO users Forum mailto:users@lists.quantum-espresso.org>>
Subject: Re: [QE-users] DFT + U not working on Sn 4d
Message-ID:
mailto:alpine.deb.2.21.1911031548430.10...@kubo.chimie.ens.fr>>
Content-Type: text/plain; charset="utf-8"; Format="flowed"


Dear ?, (please read the instructions about posting to this Forum,
signing
          and affiliation)

   Does your pseudo potential or PAW data set include the d
orbital in the
valence of the atomic species? If yes, did you check in the file
'Modules/set_hubbard_l.f90' that the l for the element in question
is set?
At least in version 6.4 of QE I did not find 'Sn'. If needed, please
modify the file, recompile and try again.

   Well, I am just guessing...

     Greetings,

        apsi


-=*=-=*

Re: [QE-users] ERROR(FoX), Cannot open file

[Pietro Davide Delugas]

Dear Ben Comer.
The flag is not valid any more. In fact It was not a fix just a 
configure option to select the old file format rather than the new one.


The old format is no longer supported, that is why the option is not 
recognized by the configure anymore.


Cannot  open file means that the program is not finding some file. Could 
you give more details on how you are running the code in order to 
understand why the error issues?


best regards - Pietro



On 11/4/19 4:56 PM, Ben Comer wrote:

Hello,

Since I've switched from espresso 5 to espresso 6.4.1 I've gotten the
"ERROR(FoX) Cannot open file" error when running across nodes. I see in
the mailing list that the prescribed fix for this is to recompile with
the "--enable-xml=no" flag in the "./configure" step. However, when I do
this I get a warning saying that the flag was not recognized and I
continue to get the error after compilation. Is there any new fix for
this issue?

Thanks,

Ben Comer
Georgia Tech

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Re: [QE-users] Installing QE_GPU

[Pietro Davide Delugas]

Dear Mohammad

You could try using the cudas runtime libraries provided with the pgi 
compiler instead the ones of your system. Besure to have all the paths 
correctly set and that no other conflicting bynary or library appears on 
the path before the right ones.


For example I used these settings ( copied from the module files 
provided with compiler)


export HOME_PGI='/opt/pgi' # this depends on where you installed the 
compiler though

export CC=$HOME_PGI/linux86-64-llvm/2019/bin/pgcc
export FC=$HOME_PGI/linux86-64-llvm/2019/bin/pgfortran
export F90=$HOME_PGI/linux86-64-llvm/2019/bin/pgf90
export F77=$HOME_PGI/linux86-64-llvm/2019/bin/pgf77

export PATH=$HOME_PGI/linux86-64-llvm/2019/bin:$PATH
export LD_LIBRARY_PATH=$HOME_PGI/linux86-64-llvm/2019/lib:$LD_LIBRARY_PATH


export PATH=$HOME_PGI/linux86-64-llvm/2019/mpi/openmpi-3.1.3/bin:$PATH
export 
LD_LIBRARY_PATH=$HOME_PGI/linux86-64-llvm/2019/mpi/openmpi-3.1.3/lib:$LD_LIBRARY_PATH 



then run pgaccelinfo to obtain the compute capilities of your card ( 
those that yoy have to pass in the configure script with the option 
-with-cuda-cc, it it the last line of the output e.g. in my case:

PGI Default Target: -ta=tesla:cc50
means that I have to use the option --with-cuda-cc=50

then run the configure ( again in my case ... )

configure --with-cuda=$HOME_PGI/pgi/linux86-64-llvm/2019/cuda/9.2 
--with-cuda-runtime=9.2 --with-cuda-cc=50 --enable-openmp 
--with-scalapack=no


the 2019 community edition provides versions 10.1 10.0 and 9.2 of cuda 
runtime libraries so you can chose the one which fits with your card.


hope that is works for you
kind regards - Pietro Delugas



On 10/27/19 3:08 PM, Mohammad Moaddeli wrote:

Dear all,

I am trying to install q-e-gpu-qe-gpu-6.4.1a1. The following PATHs are 
added in /etc/bashrc:


  CUDA  
export PATH=/usr/local/cuda-10.1/bin:$PATH
export PATH=/usr/local/cuda-10.1/include:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-10.1/lib64:$LD_LIBRARY_PATH
export 
LD_LIBRARY_PATH=/usr/local/cuda-10.1/extras/CUPTI/lib64:$LD_LIBRARY_PATH


  PGI  
PGI=/opt/pgi
export PGI
PATH=/opt/pgi/linux86-64/19.4/bin:$PATH
export PATH
PATH=/opt/pgi/linux86-64/19.4/mpi/openmpi-3.1.3/bin:$PATH
export PATH
PATH=/opt/pgi/linux86-64/19.4/mpi/openmpi-3.1.3/include:$PATH
export PATH
PATH=/opt/pgi/linux86-64/19.4/mpi/openmpi-3.1.3/lib:$PATH
export PATH
MANPATH=$MANPATH:/opt/pgi/linux86-64/19.4/man
export MANPATH

and also the Graphic Card driver is installed:

[moaddeli@localhost ~]$ nvidia-smi
Sun Oct 27 16:45:25 2019
+-+
| NVIDIA-SMI 430.50       Driver Version: 430.50       CUDA Version: 
10.1     |

|---+--+--+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile 
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util 
 Compute M. |

|===+==+==|
|   0  GeForce GTX 108...  Off  | :04:00.0  On |            N/A |
| 50%   28C    P8    10W / 250W |     58MiB / 11175MiB |  0%     
 Default |

+---+--+--+

+-+
| Processes:     GPU Memory |
|  GPU       PID   Type   Process name     Usage      |
|=|
|    0     14528      G   /usr/bin/X          39MiB |
|    0     14584      G   /usr/bin/gnome-shell          16MiB |
+-+


[root@localhost moaddeli]# lshw -numeric -C display
  *-display
       description: VGA compatible controller
       product: GP102 [GeForce GTX 1080 Ti] [10DE:1B06]
       vendor: NVIDIA Corporation [10DE]
       physical id: 0
       bus info: pci@:04:00.0
       version: a1
       width: 64 bits
       clock: 33MHz
       capabilities: pm msi pciexpress vga_controller bus_master 
cap_list rom

       configuration: driver=nvidia latency=0
       resources: iomemory:27f0-27ef iomemory:27f0-27ef irq:89 
memory:c400-c4ff memory:27fe000-27fefff 
memory:27ff000-27ff1ff ioport:c000(size=128) 
memory:c500-c507

  *-display
       description: VGA compatible controller
       product: ASPEED Graphics Family [1A03:2000]
       vendor: ASPEED Technology, Inc. [1A03]
       physical id: 0
       bus info: pci@:12:00.0
       version: 30
       width: 32 bits
       clock: 33MHz
       capabilities: pm msi vga_controller cap_list
       configuration: driver=ast latency=0
       resources: irq:16 memory:c600-c6ff 
memory:c700-c701 ioport:b000(size=128)


When I compile the code in a serial version, the executable pw.x is 
created in bin directory and seems to work well:


[moaddeli@localhost test]$ /codes/qe4/q-e-gpu-qe-gpu-6.4.1

Re: [QE-users] Structural stability problem

[Pietro Davide Delugas]

Hello
What value are you using for conv_thr in the electrons namelist ? You 
should use a value which is rather lower than the default at least 
something like 1.d-9. It this is the case the should be some warning 
just after the forces summary at the end of each force computation.

I hope this helps
Pietro


On 9/12/19 3:33 AM, Gui Wei wrote:

Dear QE users,

When I optimized the structure of a heterostructure (containing about 
130 atoms),it does converges as expected,and there is basically no 
problem with the atomic structure.The convergence threshold I used was 
*etot conv thr: 2.0D-4* *forc_conv_thr:2.0D-3*.By comparing with the 
parameter design in the literature (similar model，usually using 
software VASP),I think this convergence accuracy is relatively 
rough,especially force.So I raised the threshold to *etot conv thr: 
1.0D-4 * *forc_conv_thr:2.0D-3.*At this point I found that the 
structure optimization could not converge.I extracted the data from 
the output document and plotted Energy difference-Scf cycles curve and 
Max force-Scf cycles curve.I found that scf cycles =5 satisfies the 
convergence of the former rough convergence(both energy and 
force).After that,two curves rise synchronously,this means that the 
latter's fine convergence accuracy will never be achieved.
What I want to know is whether the atomic structure under the rough 
precision can be counted as a stable structure.If so, how do I 
understand the rise of the above two curves (this seems to be that the 
structure is not stable, in my understanding, if it is a stable 
structure, the two curves should continue to slowly decline, 
eventually reaching an almost horizontal state).If not, what is the 
solution?


Wei gui
School of Mechanical Engineering，Chongqing University, China





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Re: [QE-users] Problem about requirement on computing powers

[Pietro Davide Delugas]

Hi

- to facilitate the convergence with SrTiO3 one has usually to either 
increase the number of bands used or use   randomly generated starting 
wave functions. Try to use occupations = smearing it could help  the scf 
cycle in the first iterations.
- you are using noncollinear + spinorbit coupling, to make these 
calculation converge usually one needs to specify a starting 
magnetization in your case, if SrTiO_3 is insulating, you should try to 
initialize Ti with starting magnetization ( put it as first species and 
then put starting_magnetization = 0.1)  even if the Ti d states should 
be empty so no final magnetization should be there. Again spin orbit 
should only affect very weakly Ti d states which are empty why you do 
you need to use spin orbit to compute phono dispersion ?

- try to use occup

-   last but just because I spotted it only now the pseudopotential for 
Ti isTl.rel-pbe-dn-rrkjus_psl.1.0.0.UPF check that you are not using a 
pseudo fot Tallium instead o pseudo for Titanium


hope it helps
regards
Pietro

On 7/29/19 9:07 AM, Che Min Wu wrote:

Dear users,
I am trying to calculate phonon dispersion on SrTiO3 supercell and 
SrTiO3 slab with Quantum Espresso and thermo_pw package. However, it 
took hours to converge in each iteration of Self-consistent 
calculation, some times it even aborted because it used up 100% of CPU.


 This is my fist time calculating structure larger than an unit cell, 
I am running on a server with 16 intel I5 cpu core and 320GB of RAM. I 
ran it with command
mpirun -np 4 $BIN_DIR/thermo_pw.x < srtio3_slab.in 
 > srtio3_slab.out
I wonder if it is me doing things wrong, or is it simply impossible to 
do these calculation with my computing power.

I have attached my input file , thanks for any reply or suggestion.

Thanks and Regards
Che Min Wu

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Re: [QE-users] Question about restarting relaxation jobs

[Pietro Davide Delugas]

Hello

1)  and 2) PW writes the restart files only when it terminates before 
convergence is reached either because the max number of steps (and the  
max number may be either the number of  electronic steps during scf of  
number of ionic steps during structural relaxation) or the the execution 
time exceed  max_seconds specified in input or because the user has 
stopped the calculation creating a file in the outdir called prefix.EXIT.


If restart_mode in &control is set to "restart"  pw will try to restart 
the relaxation from the last POSITIONS  which have been saved in the 
prefix.save directory using the last saved charge density and wave 
functions. If it finds the restart files it will use them also. This 
mechanism works fine if positions, charge density and wave functions  
data have been saved regularly,  but if the calculation is going to be 
stopped abruptly, for example by the job manager,  there is no way to 
prevent that the stop arrives when the program is writing these data. 
The safer way to go when you are using a job manager is to set the 
max_seconds variable to a number consistently lower than the time 
allocated by the job manager, the difference between these two times 
should be enough to allow to the program to pass through one of the 
check_points at which, during execution, it checks if the execution time 
has exceeded the max_seconds s or if the user has created a prefix.EXIT 
file. To estimate how long should be the difference between max_seconds 
and the scheduled execution time check how long it takes to the program 
to make an scf loop, this one will  a very safe estimate, you could 
reduce this time significantly and things should be working.




3) I don't understans what you want to do. You create the prefix.EXIT 
file when you want to stop your calculation and you want the calculation 
to finish smoothly saving all restart information so that it can 
resatart from more or less the same point when it was interrupted. It is 
completely senseless to rename  the output file as prefix.EXIT because 
it will make the program to stop as soon as a check_point detects the 
file and the file will be deleted. The only thing that you have to do 
when restarting a calculation is


 *    Specify restart_mode = 'restart' in the input.in file

 *    take care that the information saved in output.out is not
   rewritten by the new execution just use something as mpirun pw.x 
   < input.in >> output.out which appends the new output to the old one
   or redirect the output to files with different names

4)   outdir must be the same or if you want to use a different one you 
have to create the new outdir befor restarting and copy there all the 
data of the previous calculation i.e. the prefix.save directory.



5) don't complicate things too much



Pietro



On 7/6/19 3:59 PM, Yeon, Jejoon wrote:


Hello


I have very small amount of experience using QE, so please excuse my 
beginner question. I'm about to start relaxation of big crystal 
structure, and I wish to make my QE relaxation jobs ready for restart. 
Here are my questions:



1) According to "restarting" section from manual, 
(https://www.quantum-espresso.org/Doc/pw_user_guide/node20.html) it 
seems that QE does not creates the dedicated restart file, is this 
correct?



2) If I set up "max_seconds" option as 604800 seconds (1 week), and 
request wall time to server 1 week, do my calculation jobs are ready 
to restart after 1 week? (1 week is just example but our server 
cluster have maximum some walltime limitation, and I don't think any 
of my relaxation works will be finished within that time. ) Also, does 
this "max_seconds" option must be required to restart?


3) When I execute QE in the submit script, I use something similar as:
mpirun pw.x  < input.in > output.out
In this case, if the relaxation job is killed due to wall time limit 
(without setting max_seconds), can I just change the name of the 
output.out to prefix.EXIT, (of course I set up prefix in the input 
file) and then include restart_mode = "restart" in the input file, 
then submit a job for restart?
I have old files which are finished after reaching wall time limit 
without "max_seconds" option, and I'm curious if I can use those files 
to restart.


4) I also use outdir option in the input file, does the outdir option 
should be the same when restart?


5) Are there any other things or useful hints that I need to consider 
when restart?


Thank you


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Re: [QE-users] phonon frequencies at Gamma using qplot = .true. along K-Gamma-L

[Pietro Davide Delugas]

Thanks for reporting
this is a bug, I started an issue on the GitLab repository. If you are 
interested you may follow the discussion here.


Thanks again
Pietro


On 6/23/19 8:55 PM, Hari Paudyal wrote:

Dear experts,

To calculate the phonon along a specific path of BZ (K-Gamma-L) for 
Si, I used  qplot = .true. and q_in_band_form = .true.  (taking 2 
points in between).  Surprisingly, I got the following frequencies at 
Gamma,

     q = (    0.0   0.0   0.0 )

 **
     freq (    1) =      11.535533 [THz] =     384.783979 [cm-1]
     freq (    2) =      11.535533 [THz] =     384.783979 [cm-1]
     freq (    3) =      11.535533 [THz] =     384.783979 [cm-1]
     freq (    4) =      18.554595 [THz] =     618.914662 [cm-1]
     freq (    5) =      18.554595 [THz] =     618.914662 [cm-1]
     freq (    6) =      18.554595 [THz] =     618.914662 [cm-1]
 **

On the other hand, If I calculate only at Gamma point, I get
     q = (    0.0   0.0   0.0 )

 **
     freq (    1) =      -0.117104 [THz] =      -3.906180 [cm-1]
     freq (    2) =      -0.117104 [THz] =      -3.906180 [cm-1]
     freq (    3) =      -0.117104 [THz] =      -3.906180 [cm-1]
     freq (    4) =      15.035771 [THz] =     501.539319 [cm-1]
     freq (    5) =      15.035771 [THz] =     501.539319 [cm-1]
     freq (    6) =      15.035771 [THz] =     501.539319 [cm-1]
 **

Why am I getting the large frequencies at Gamma if I calculate along 
K-Gamma-L? Do I need to specify Gamma always in the first?Why?


My input files for the scf and phonon for Si are as the following.

 &control
    calculation     = 'scf'
    prefix          = 'Si'
    restart_mode    = 'from_scratch'
    wf_collect      = .true.
    pseudo_dir      = './'
    outdir          = './'
 /
 &system
    ibrav           = 2
    celldm(1)       = 10.261217
    nat             = 2
    ntyp            = 1
    ecutwfc         = 45.0
 /
 &electrons
    diagonalization = 'david'
    mixing_beta     = 0.3
    conv_thr        = 1.0d-10
/
ATOMIC_SPECIES
  Si  28.0855  Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
  Si  0.00  0.00  0.00
  Si  0.25  0.25  0.25
K_POINTS automatic
8 8 8 0 0 0

Si
&inputph
 outdir    = './',
 prefix    = 'Si',
 fildyn    = 'Si.dyn',
 fildvscf  = 'dvscf',
 ldisp     = .true.,
 tr2_ph    = 1.0d-14
 qplot     = .true.
 q_in_band_form = .true.
/
3
-0.750   0.750   0.000   2   ! K
 0.000   0.000   0.000   2   ! G
-0.500   0.500   0.500   1   ! L

Thank You,
Hari Paudyal
SUNY Binghamton

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Re: [QE-users] Relaxation of CaCO3

[Pietro Davide Delugas]

Hello
conv_thr = 1.d-6 is most likely too high, and forces are not accurate 
enough, if it is the case, the program is actually warning you about 
this just  after reporting the forces, and suggesting  you to decrease 
the  threshold. Check the output. If it is the case,  decrease conv_thr 
;  I think that 1.d-8 could be low enough unless you are already close 
to the minimum.





On 05/31/2019 12:11 PM, Hassan Ahmed Mohammed wrote:

Hello Pietro,
I'm sorry that was not clear in my question because i'm totally new to QE.
Yes, the structural relaxation


On Fri, May 31, 2019 at 5:00 AM 
<mailto:users-requ...@lists.quantum-espresso.org>> wrote:


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Today's Topics:

   1. Oxygen PAW Pseudopotentials have 3d core electrons. (Amreen
Bano)
   2. parallelization of pw.x (Michal Krompiec)
   3. Re: parallelization of pw.x (Giuseppe Mattioli)
   4. Re: parallelization of pw.x (Pietro Delugas)
   5. Re: parallelization of pw.x (Michal Krompiec)
   6. Re: Output files for ph.x (Appleton, Robert J)
   7. Re: Output files for ph.x (Paolo Giannozzi)
   8. Re: higher total energy in the last stage of vc-relax (Kevin
May)
   9. Core wavefunction (emin klc)
  10. Re: Oxygen PAW Pseudopotentials have 3d core electrons.
      (Paolo Giannozzi)
  11. Large input problem (???)
  12. Relaxation of CaCO3 (Hassan Ahmed Mohammed)
  13. Re: Relaxation of CaCO3 (Pietro Davide Delugas)


--

Message: 1
Date: Thu, 30 May 2019 08:53:55 -0500
From: Amreen Bano mailto:banoamree...@gmail.com>>
To: users@lists.quantum-espresso.org
<mailto:users@lists.quantum-espresso.org>
Subject: [QE-users] Oxygen PAW Pseudopotentials have 3d core
        electrons.
Message-ID:
       
mailto:e0rqk-xpa3wsovvsoeqayepcyly...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Dear all,

I am working Oxygen based clusters. After performing the Pdos
calculation i
found that O-3d states are also present. Why this is so? Is this
an error
in the PP file or something else. Kindly suggest me the if there
is any
problem with this PP.

Thanks in advance.
Amreen.
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Message: 2
Date: Thu, 30 May 2019 15:42:18 +0100
From: Michal Krompiec mailto:michal.kromp...@gmail.com>>
To: Quantum Espresso users Forum mailto:users@lists.quantum-espresso.org>>
Subject: [QE-users] parallelization of pw.x
Message-ID:
       
mailto:caowossppcqz4ntjirqi30hm5kqnyqrr5e-40u_2ropo2nqx...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Hello,
I am trying to run a calculation on a 2D slab with a bit of
adsorbate (119
atoms in total), and I would like to parallelize it as much as
possible. I
am using a 3 3 1 Monkhorst-Pack grid (so I have 5 k-points).
I tried using -npool 5 -nt 4 using 20 MPI processes and 5 threads per
process but, as it seems, the speedup was just 3.7x:
   PWSCF        :   1d 4h27m CPU      7h43m WALL
What could have gone wrong, is there anything "obvious" I can do to
diagnose the problem? I am using QE 6.4rc, compiled with gcc and
OpenMPI,
without ELPA.

Best regards,

Michal Krompiec

Merck KGaA and University of Southampton
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Message: 3
Date: Thu, 30 May 2019 17:14:44 +0200
From: Giuseppe Mattioli mailto:giuseppe.matti...@ism.cnr.it>>
To: Quantum ESPRESSO users Forum mailto:users@lists.quantum-espresso.org>>
Subject: Re: [QE-users] parallelization of pw.x
Message-ID:
       
<20190530171444.horde.la-caab3_eji1ko_pwre...

Re: [QE-users] Relaxation of CaCO3

[Pietro Davide Delugas]

Hello
did not converge what ? the structural relaxation or the self consistency ?

it is hard to say anything without have more information.
Pietro


On 05/31/2019 11:17 AM, Hassan Ahmed Mohammed wrote:


Hello all,
I'm trying to study the adsorption of different compounds on a calcite 
slab. I have been trying to do geometry relaxation for the calcite 
using QE and used burai to generate the input file. It worked for a 
long time but it did not converge. I tried several times with changes 
such as using kpoints instead of gamma, using other pseudopotentials 
but no luck.

I appreciate any suggestions or ideas that could lead to my mistake!
Here is my input file

&CONTROL
calculation = "relax"
forc_conv_thr = 1.0e-03
max_seconds = 1.72800e+05
nstep = 100
pseudo_dir = "."
tprnfor = .TRUE.
tstress = .TRUE.
/
&SYSTEM
a = 3.30600e+01
b = 1.45800e+01
c = 4.87600e+01
degauss = 1.0e-02
ecutrho = 2.25000e+02
ecutwfc = 2.5e+01
ibrav = 8
nat = 480
ntyp = 3
occupations = "smearing"
smearing = "gaussian"
/
&ELECTRONS
conv_thr = 1.0e-06
electron_maxstep = 200
mixing_beta = 7.0e-01
startingpot = "atomic"
startingwfc = "atomic+random"
/
&IONS
ion_dynamics = "bfgs"
/
&CELL
/
K_POINTS {gamma}

ATOMIC_SPECIES
Ca 40.07800 Ca.pbe-nsp-van.UPF
C 12.01070 C.pbe-rrkjus.UPF
O 15.99940 O.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
Ca 25.034002 5.792000 9.889249
.

.






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Re: [QE-users] Enquiry about the Choice for the Pseudopotential

[Pietro Davide Delugas]

  Dear Kenan

when you send attachment via dropbox it would be much  easier for the 
other users to read them if you collected them in an archive and sent a 
link to the archive directly in the main message.

kind regards - Pietro



On 04/15/2019 01:26 PM, Kenan Song wrote:

Dear Sir/Madam,

I used Quantum Espresso (QE) to compute the band structure for the 
same system that I examined by VASP but QE gives me very different 
band structure from that given by VASP, including both of the band 
shape and energy.


I think that the remain reason comes from the pseudopotential I choose 
is not proper. VASP provides the pseudopotential for Co element with 9 
valence electron; while, QE provides one with 27 valence electrons. 
Would you anyone please tell me how to choose or generate a proper 
pseudopotential? Thank you.


Kind regards,

Kenan Song


This message and its contents, including attachments are intended 
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Re: [QE-users] Compilation on a server ends with error 1

[Pietro Davide Delugas]

Dear Paolo

:) many compliments to your system administrator ...

this is yet an other issue with a too compiler version. It is very 
likely the case that your mpif90 is still using fortran 4.4.6 just check 
with mpif90 --version  and see what it prints out.
If mpif90 is using 5.4 the simpler thing to do is to oblige the 
compiler, and change line 58 of PP/src/plotband.f90 from


CHARACTER(len=:), ALLOCATABLE :: line

to

CHARACTER(len=2048), ALLOCATABLE :: line

and anything should be working. You can meet other errors of this kind, 
read carefully the error messages and try to fix them.


In the case ( I am afraid it is actually the case) that mpif90 is using 
the old fortran version, you need to install an  mpi library that uses 
your desired gfortran version.


It is a little bit complicated but not very difficult, just takes a bit 
of time and patience,  you have just to download the source, better a 
not too old or not too new one , for example this one should work:


https://download.open-mpi.org/release/open-mpi/v2.0/openmpi-2.0.4.tar.gz

follow configure instructions taking care to enable f90 API and to   
point  to the right fortran compiler.
It's up to you to decide whether it takes less time doing this  by 
yourself,  or convince the system administrator to help you ...

best wishes
Pietro





On 04/08/2019 01:53 AM, Fabio Costa wrote:

Dear Paolo and Pietro

Thanks for the assistance, and sorry for the late reply on your advice.

I contacted the system administrator, and he explained to me that as 
there are several other applications running under this old gfortran 
version, and because of that he could not just issue "sudo apt update 
gfortran", on the risk of messing up with all the other stuff 
currently running on the system. His advice to me was to manually 
install a newer version inside my workspace.


I did that, and now I have both the native 4.4.6 and the 5.4.0 
gfortran compilers. I also added to my bashrc the line "export 
F90=/path/to/gfortran5.4.0/". When i run configure, it detects the 
gfortran v5.4.0, so I think that I did this right. At first, make all 
still crashes at phcg.x. I proceeded changing the lines in Makefile as 
Pietro sugested, and when compiling again it goes a bit further, but 
still crashes. To avoid these crashes, I tryed to compile just the 
packages I'm intending to use (pw, ph, w90 and epw). By issuing make 
pw, followed by make ph, make w90, the task is succesful, but It 
craches again when I issue make epw. The print screen of the error 
message is in the link: https://imgur.com/CerJStE .


Also, I'm still getting the same errors with the compiled executables. 
About Paolo's advice, in my current situation, where I cant just 
update the whole thing, and kinda have two version of gfortran. I'm 
not sure if the crashes are because when  the executables run, they 
are still linking to the gfortran 4.4.6. What course of action would 
you sugest?


Thank you for the assistance

Fábio Costa
MSc student in physics
Federal University of Bahia, Brazil


*De:* users  em nome de 
Paolo Giannozzi 

*Enviado:* quinta-feira, 28 de março de 2019 11:40
*Para:* Quantum Espresso users Forum
*Assunto:* Re: [QE-users] Compilation on a server ends with error 1
There are two unrelated problems:
- the linker is unable to find the main program in PHonon/Gamma. I 
have never seen this happen before, but the link is done in a slightly 
different way from all other cases and this will be fixed
- the executable doesn't work likely due to a known problem of many 
old compilers with unallocated optional variables


Paolo


On Thu, Mar 28, 2019 at 3:47 AM Fabio Costa > wrote:


Dear all

I'm trying to install QE-6.4 on a server, by doing the usual
procedure, ./configure and make all commands.

The configure step seems to be successful, but the compilation
fails after a couple minutes, with a message "make: *** [ph] Error
1". Even with this interruption, a few .x files are compiled, such
as pw.x, ph.x, etc., but when I try to run a calculation, It also
results in an error message.

Appologies for my not-so-much enlightening description, as I
myself could not extract many info from the error messages, so I
hope the print screens will be more helpfull than I could.

https://imgur.com/HeT8JMM
https://imgur.com/ZyyVGt3
https://imgur.com/DyYlO4R

Thanks in advance for any assistance

Fábio Costa
MSc student in physics
Federal University of Bahia, Brazil


Imgur 
Compilation error
imgur.com 




Imgur 
configure output
imgur.com 




Imgur 
pw.x error
   

Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

Hi

at a quick glance the reduce_io affects only io_level of the band 
structure calculation started by run_nscf, so yes no problem in any case 
for which band structure calculation is not performed.


I should have neutralized the problem in the delvopment version, now 
reduce_io sets to 1 io_level of band computations, the issue is solved, 
reduce_io is now kind of useless but doesn't hurt.


If you want to  continue doing testing on the subject you are welcome,  
but you should use the development version ( and yes update the subject )


thanks and regards - Pietro


On 03/28/2019 09:47 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/27/19 12:02 PM, Pietro Davide Delugas wrote:

Yes you are right.
reduce_io shouldn't be used anymore in ph.x  input
Pietro

I'm doing some more tests and will report soon another time ... but in 
short:


It seems that the flag reduce_io leads to error only in single-q, 
not-Gamma calculation. You can use it in single-q, at Gamma, and on 
any q when in dispersion mode, within grid approach).


Should I open another thread (sorry if I'm mixing different subjects) 
... or reduce_io will be  "DEPRECATED" from now, and I should stop 
boring you guys.


Best,


On 03/26/2019 05:11 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 1:02 PM, Pietro Davide Delugas wrote:
sorry are you still talking of ph.x with grid as in the beginning 
of the thread or ph.x in general ?
I guess (maybe, I wrong about it) it is for both cases, as the wfcs 
and bands computed when ph.x calls pw.x, data necessary for 
perturbation, are not saved in disk (in /scratch/_ph0/), nor in RAM 
(or maybe, it is in the RAM, but the codes looks for data in disk).


Best,



On 03/26/2019 04:39 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,


On 3/26/19 11:26 AM, Pietro Davide Delugas wrote:
I don't know whether the fact that the restart does not work with 
reduce_io = .true. may be considered as a bug or as a feature.
But as it is, I guess there is no way to use the reduce_io true. 
In my case, there is no recover = .true. (a restart) in the input:


ph0
&inputph
  prefix='test',
  reduce_io = .true.
  trans =.true.
  outdir='scratch',
  fildyn='test.dyn',
/
0.009443  0.016356  0.00

And the output (main parts, I guess):
 Program PHONON v.6.4 starts on 26Mar2019 at  9:33: 7
 Reading data from directory:
 scratch/acnl1.save/
 2D2D2D2D2D2D2D2D2D2D2D2D 


  The code is running with the 2D cutoff
 Calculation of q =    0.0094430   0.0163560 0.000
 Subspace diagonalization in iterative solution of the 
eigenvalue problem:

 a serial algorithm will be used
 Title:
 ph0
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

 Starting wfcs are   16 atomic wfcs
 End of band structure calculation
 ph0
 Computing dynamical matrix for
    q = (   0.0094430   0.0163560 0.000 )
 Error in routine openfilq (1):
 file acnl1.wfc not found

When commenting the reduce_io, all goes normal; it continues the 
"Computing dynamical matrix for" and computes the phonon frequencies.


Best,


In the second case we should warn the user about it in the 
documentation



On 03/26/2019 02:58 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 10:32 AM, Pietro Davide Delugas wrote:

sorry but your message is painfully impervious  ...

Sorry ...


do  I understand correctly that at the moment,   the only issue 
is that at restart ph fails when the reduce_io flag is set to 
true.

 Is it right ?
Yes, because when the reduce_io is true, the code do not save 
the bands and wfcs in the RAM, and the dfpt step ends with


 Error in routine openfilq (1):
 file acnl1.wfc not found

After recalculate the bands, in the part
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

there is no:
 Writing output data file acnl1.save/

As there is when the reduce io is false.

Best,


Pietro

On 03/26/2019 02:16 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

I just compiled the q-e-dev to try the changes from 
https://gitlab.com/QEF/q-e/issues/102


It appears some things are missing (could be may fault). The 
scf (wf_collect false, 2D) wrote the wfcs, xml and bands on 
scratch. The ph0(reduce_io true, single-q out Gamma) created 
the phsave and save in _ph0, and copied only charge.dat to 
_ph0/save; no wfcs, nor xml in _ph0.In the phout, there is no 
"failed retrieving info from xml", it found the bands in 
scratch/save and printed (reading from /scratch/xml? as there 
is no xml in _ph0?) it is a 2D calc. It built the pot from 
_ph0/save (the charge.dat is there) did the scf, but forgot to 
write the wfcs from this scf (and apparently, did not stored 
it on RAM) ... going on, the dfpt step could not find the .wfc 
(is

Re: [QE-users] Compilation on a server ends with error 1

[Pietro Davide Delugas]

Hi Fabio

I am noticing now that you are also using a very old version of the 
gfortran compiler (4.4.6) .
You should use a newer version, anything like 4.8 or newer should work 
fine.

Pietro

On 03/28/2019 03:47 AM, Fabio Costa wrote:

Dear all

I'm trying to install QE-6.4 on a server, by doing the usual 
procedure, ./configure and make all commands.


The configure step seems to be successful, but the compilation fails 
after a couple minutes, with a message "make: *** [ph] Error 1". Even 
with this interruption, a few .x files are compiled, such as pw.x, 
ph.x, etc., but when I try to run a calculation, It also results in an 
error message.


Appologies for my not-so-much enlightening description, as I myself 
could not extract many info from the error messages, so I hope the 
print screens will be more helpfull than I could.


https://imgur.com/HeT8JMM
https://imgur.com/ZyyVGt3
https://imgur.com/DyYlO4R

Thanks in advance for any assistance

Fábio Costa
MSc student in physics
Federal University of Bahia, Brazil


Imgur 
Compilation error
imgur.com 




Imgur 
configure output
imgur.com 




Imgur 
pw.x error
imgur.com 






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Re: [QE-users] incorrect LO-TO splitting for CaO and MgO

[Pietro Davide Delugas]

Hi Casey
using your inputs cut and paste I get the right values.

# mode   [cm-1]    [THz]  IR
    1 -0.00   -0.    0.
    2 -0.00   -0.    0.
    3  0.00    0.    0.
    4    291.10    8.7268   11.3884
    5    291.10    8.7268   11.3884
    6    569.57   17.0753   11.3884

What version are you using ?


On 03/27/2019 03:19 PM, Casey Brock wrote:
I am using pw.x -> ph.x -> dynmat.x to get the LO and TO phonon 
frequencies at gamma for rock-salt CaO. The value for the LO phonon I 
am getting differs from experiment and other DFPT calculations in the 
literature by 5 THz (167 cm^-1). Perhaps this is a problem with 
Quantum Espresso, but it’s very possible I’m doing something wrong. 
I’ve included results and input files below, and any advice would be 
greatly appreciated.


The TO and LO frequencies in THz are given below. Notice that Quantum 
Espresso using DFPT gives a value that is too low.

experiment: 8.9, 17.1
frozen phonon (Phonopy + Quantum Espresso): 8.71, 17.1
DFPT (Quantum Espresso, pw.x->ph.x->dynmat.x):  8.53, *12.2*
*
*
If I use Phonopy (frozen phonon technique) combined with Quantum 
Espresso (pw.x and ph.x) I get the correct splitting at gamma. I have 
tried the same calculation with MgO and I see the same problem, where 
the frozen phonon technique works while DFPT does not. Here are some 
things I have tried: different PAW pseudopotentials, increasing 
ecutwfc and ecutrho, increasing k-points, reducing conv_thr, and 
reducing tr2_ph.


Thanks in advance,
Casey Brock

input to pw.x
---
&control
    calculation='scf'
    restart_mode='from_scratch'
    prefix='cao'
    pseudo_dir = './'
    outdir='./output/'
    tprnfor = .true.
    tstress = .true.
/
&system
    ibrav = 0
    nat = 2
    ntyp = 2
    ecutwfc = 70.0
    ecutrho = 280.0
/
&electrons
   conv_thr =  1.0d-10
   mixing_beta = 0.7
/
K_POINTS {automatic}
 12 12 12 0 0 0

CELL_PARAMETERS bohr
 4.45 4.45 0
 0 4.45 4.45
 4.45 0 4.45
ATOMIC_SPECIES
 O  16.00 O.pz-n-kjpaw_psl.0.1.UPF
 Ca 40.08 Ca.pz-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Ca  0.0  0.0  0.0
O   0.5  0.5  0.5

input to ph.x
---
Phonon for CaO
&inputph
 prefix='cao',
 outdir='./output/',
 fildyn='dyn.G'
 epsil = .true.
 tr2_ph=1.0d-14,
/
0 0 0

input to dynmat.x
---
&input
 fildyn = 'dyn.G'
 asr = 'simple'
 q(1)=0.0, q(2)=0.0, q(3)=1.0
/



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Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

Yes you are right.
reduce_io shouldn't be used anymore in ph.x  input
Pietro

On 03/26/2019 05:11 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 1:02 PM, Pietro Davide Delugas wrote:
sorry are you still talking of ph.x with grid as in the beginning of 
the thread or ph.x in general ?
I guess (maybe, I wrong about it) it is for both cases, as the wfcs 
and bands computed when ph.x calls pw.x, data necessary for 
perturbation, are not saved in disk (in /scratch/_ph0/), nor in RAM 
(or maybe, it is in the RAM, but the codes looks for data in disk).


Best,



On 03/26/2019 04:39 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,


On 3/26/19 11:26 AM, Pietro Davide Delugas wrote:
I don't know whether the fact that the restart does not work with 
reduce_io = .true. may be considered as a bug or as a feature.
But as it is, I guess there is no way to use the reduce_io true. In 
my case, there is no recover = .true. (a restart) in the input:


ph0
&inputph
  prefix='test',
  reduce_io = .true.
  trans =.true.
  outdir='scratch',
  fildyn='test.dyn',
/
0.009443  0.016356  0.00

And the output (main parts, I guess):
 Program PHONON v.6.4 starts on 26Mar2019 at  9:33: 7
 Reading data from directory:
 scratch/acnl1.save/
 2D2D2D2D2D2D2D2D2D2D2D2D 


  The code is running with the 2D cutoff
 Calculation of q =    0.0094430   0.0163560   0.000
 Subspace diagonalization in iterative solution of the 
eigenvalue problem:

 a serial algorithm will be used
 Title:
 ph0
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

 Starting wfcs are   16 atomic wfcs
 End of band structure calculation
 ph0
 Computing dynamical matrix for
    q = (   0.0094430   0.0163560   0.000 )
 Error in routine openfilq (1):
 file acnl1.wfc not found

When commenting the reduce_io, all goes normal; it continues the 
"Computing dynamical matrix for" and computes the phonon frequencies.


Best,


In the second case we should warn the user about it in the 
documentation



On 03/26/2019 02:58 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 10:32 AM, Pietro Davide Delugas wrote:

sorry but your message is painfully impervious  ...

Sorry ...


do  I understand correctly that at the moment,   the only issue 
is that at restart ph fails when the reduce_io flag is set to true.

 Is it right ?
Yes, because when the reduce_io is true, the code do not save the 
bands and wfcs in the RAM, and the dfpt step ends with


 Error in routine openfilq (1):
 file acnl1.wfc not found

After recalculate the bands, in the part
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

there is no:
 Writing output data file acnl1.save/

As there is when the reduce io is false.

Best,


Pietro

On 03/26/2019 02:16 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

I just compiled the q-e-dev to try the changes from 
https://gitlab.com/QEF/q-e/issues/102


It appears some things are missing (could be may fault). The scf 
(wf_collect false, 2D) wrote the wfcs, xml and bands on scratch. 
The ph0(reduce_io true, single-q out Gamma) created the phsave 
and save in _ph0, and copied only charge.dat to _ph0/save; no 
wfcs, nor xml in _ph0.In the phout, there is no "failed 
retrieving info from xml", it found the bands in scratch/save 
and printed (reading from /scratch/xml? as there is no xml in 
_ph0?) it is a 2D calc. It built the pot from _ph0/save (the 
charge.dat is there) did the scf, but forgot to write the wfcs 
from this scf (and apparently, did not stored it on RAM) ... 
going on, the dfpt step could not find the .wfc (is it a miss 
behave of the reduce io flag? previously, in a single 
calculation with reduce io flag it did not happen). I repeated 
the ph0 with the reduce io flag commented, and as results: the 
wfc are in _ph0, the xml in _ph0/save, after the phx calls pwx 
to calc the bands it wrote it, and the dfpt now finds the wfcs.


Best,















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Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

sorry are you still talking of ph.x with grid as in the beginning of the 
thread or ph.x in general ?



On 03/26/2019 04:39 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,


On 3/26/19 11:26 AM, Pietro Davide Delugas wrote:
I don't know whether the fact that the restart does not work with 
reduce_io = .true. may be considered as a bug or as a feature.
But as it is, I guess there is no way to use the reduce_io true. In my 
case, there is no recover = .true. (a restart) in the input:


ph0
&inputph
  prefix='test',
  reduce_io = .true.
  trans =.true.
  outdir='scratch',
  fildyn='test.dyn',
/
0.009443  0.016356  0.00

And the output (main parts, I guess):
 Program PHONON v.6.4 starts on 26Mar2019 at  9:33: 7
 Reading data from directory:
 scratch/acnl1.save/
 2D2D2D2D2D2D2D2D2D2D2D2D
  The code is running with the 2D cutoff
 Calculation of q =    0.0094430   0.0163560   0.000
 Subspace diagonalization in iterative solution of the eigenvalue 
problem:

 a serial algorithm will be used
 Title:
 ph0
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

 Starting wfcs are   16 atomic wfcs
 End of band structure calculation
 ph0
 Computing dynamical matrix for
    q = (   0.0094430   0.0163560   0.000 )
 Error in routine openfilq (1):
 file acnl1.wfc not found

When commenting the reduce_io, all goes normal; it continues the 
"Computing dynamical matrix for" and computes the phonon frequencies.


Best,


In the second case we should warn the user about it in the documentation


On 03/26/2019 02:58 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 10:32 AM, Pietro Davide Delugas wrote:

sorry but your message is painfully impervious  ...

Sorry ...


do  I understand correctly that at the moment,   the only issue is 
that at restart ph fails when the  reduce_io flag is set to true.

 Is it right ?
Yes, because when the reduce_io is true, the code do not save the 
bands and wfcs in the RAM, and the dfpt step ends with


 Error in routine openfilq (1):
 file acnl1.wfc not found

After recalculate the bands, in the part
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

there is no:
 Writing output data file acnl1.save/

As there is when the reduce io is false.

Best,


Pietro

On 03/26/2019 02:16 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

I just compiled the q-e-dev to try the changes from 
https://gitlab.com/QEF/q-e/issues/102


It appears some things are missing (could be may fault). The scf 
(wf_collect false, 2D) wrote the wfcs, xml and bands on scratch. 
The ph0(reduce_io true, single-q out Gamma) created the phsave and 
save in _ph0, and copied only charge.dat to _ph0/save; no wfcs, 
nor xml in _ph0.In the phout, there is no "failed retrieving info 
from xml", it found the bands in scratch/save and printed (reading 
from /scratch/xml? as there is no xml in _ph0?) it is a 2D calc. 
It built the pot from _ph0/save (the charge.dat is there) did the 
scf, but forgot to write the wfcs from this scf (and apparently, 
did not stored it on RAM) ... going on, the dfpt step could not 
find the .wfc (is it a miss behave of the reduce io flag? 
previously, in a single calculation with reduce io flag it did not 
happen). I repeated the ph0 with the reduce io flag commented, and 
as results: the wfc are in _ph0, the xml in _ph0/save, after the 
phx calls pwx to calc the bands it wrote it, and the dfpt now 
finds the wfcs.


Best,











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Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

I don't know whether the fact that the restart does not work with 
reduce_io = .true. may be considered as a bug or as a feature.

In the second case we should warn the user about it in the documentation


On 03/26/2019 02:58 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

On 3/26/19 10:32 AM, Pietro Davide Delugas wrote:

sorry but your message is painfully impervious  ...

Sorry ...


do  I understand correctly that at the moment,   the only issue is 
that at restart ph fails when the  reduce_io flag is set to true.

 Is it right ?
Yes, because when the reduce_io is true, the code do not save the 
bands and wfcs in the RAM, and the dfpt step ends with


 Error in routine openfilq (1):
 file acnl1.wfc not found

After recalculate the bands, in the part
 The potential is recalculated from file :
 scratch/_ph0/acnl1.save/charge-density

there is no:
 Writing output data file acnl1.save/

As there is when the reduce io is false.

Best,


Pietro

On 03/26/2019 02:16 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

I just compiled the q-e-dev to try the changes from 
https://gitlab.com/QEF/q-e/issues/102


It appears some things are missing (could be may fault). The scf 
(wf_collect false, 2D) wrote the wfcs, xml and bands on scratch. The 
ph0(reduce_io true, single-q out Gamma) created the phsave and save 
in _ph0, and copied only charge.dat to _ph0/save; no wfcs, nor xml 
in _ph0.In the phout, there is no "failed retrieving info from xml", 
it found the bands in scratch/save and printed (reading from 
/scratch/xml? as there is no xml in _ph0?) it is a 2D calc. It built 
the pot from _ph0/save (the charge.dat is there) did the scf, but 
forgot to write the wfcs from this scf (and apparently, did not 
stored it on RAM) ... going on, the dfpt step could not find the 
.wfc (is it a miss behave of the reduce io flag? previously, in a 
single calculation with reduce io flag it did not happen). I 
repeated the ph0 with the reduce io flag commented, and as results: 
the wfc are in _ph0, the xml in _ph0/save, after the phx calls pwx 
to calc the bands it wrote it, and the dfpt now finds the wfcs.


Best,







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Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

sorry but your message is painfully impervious  ...
do  I understand correctly that at the moment,   the only issue is that 
at restart ph fails when the  reduce_io flag is set to true.

 Is it right ?
Pietro

On 03/26/2019 02:16 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

I just compiled the q-e-dev to try the changes from 
https://gitlab.com/QEF/q-e/issues/102


It appears some things are missing (could be may fault). The scf 
(wf_collect false, 2D) wrote the wfcs, xml and bands on scratch. The 
ph0(reduce_io true, single-q out Gamma) created the phsave and save in 
_ph0, and copied only charge.dat to _ph0/save; no wfcs, nor xml in 
_ph0.In the phout, there is no "failed retrieving info from xml", it 
found the bands in scratch/save and printed (reading from 
/scratch/xml? as there is no xml in _ph0?) it is a 2D calc. It built 
the pot from _ph0/save (the charge.dat is there) did the scf, but 
forgot to write the wfcs from this scf (and apparently, did not stored 
it on RAM) ... going on, the dfpt step could not find the .wfc (is it 
a miss behave of the reduce io flag? previously, in a single 
calculation with reduce io flag it did not happen). I repeated the ph0 
with the reduce io flag commented, and as results: the wfc are in 
_ph0, the xml in _ph0/save, after the phx calls pwx to calc the bands 
it wrote it, and the dfpt now finds the wfcs.


Best,



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Re: [QE-users] pw.x prints the first few lines and segmentation fault

[Pietro Davide Delugas]

Hello
could you try the attached  patch  ?

copy the file in the q-e topdir and type

patch -p1 --merge < patch_old_intel

in case you wanted to undo the patch

patch -R -p1 --merge < patch_old_intel

please let me know  if it works
regards  Pietro

On 03/22/2019 04:56 PM, Paolo Giannozzi wrote:
Some versions of the intel compiler miscompile the recently modified 
XML code. A patch will be released soon. Your make.inc is perfectly fine

Paolo


On Fri, Mar 22, 2019 at 4:42 PM Hari Paudyal > wrote:


Dear experts,

After the successful installation of qe-v6.4, pw.x gives
segmentation fault after when it prints the first few lines as;

     Parallel version (MPI), running on     1 processors

     MPI processes distributed on     1 nodes
     Waiting for input...
     Reading input from standard input

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  4
     Max angular momentum in pseudopotentials (lmaxx) =  3
forrtl: severe (174): SIGSEGV, segmentation fault occurred

I had no problem compiling/running all the previous versions (even
some of the development versions I have installed on 15Oct2018,
20Jan2019). Since I am not an expert, I do not know what has been
changed in the process of installation in this new released
version v6.4, but I am pretty sure that nothing has been changed
in my cluster regarding compilers/libraries. For info, I am using
intel/composer_xe_2013.1.117.

Further, If I look more carefully to the make.inc files generated
after ./configure between qe-v6.3 and qe-v6.4, I found the
following differences;

# TOPDIR = /home/hari/qe-6.3
DFLAGS         =  -D__FFTW -D__MPI
LIBS           = $(CUDA_LIBS) $(SCALAPACK_LIBS) $(LAPACK_LIBS)
$(FOX_LIB) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS)
$(HDF5_LIB) $(LD_LIBS)
# Install directory - not currently used

# TOPDIR = /home/hari/qe-6.4
DFLAGS         =  -D__DFTI -D__MPI
LIBXC_LIBS     =
QELIBS         = $(CUDA_LIBS) $(SCALAPACK_LIBS) $(LAPACK_LIBS)
$(FOX_LIB) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS)
$(HDF5_LIB) $(LIBXC_LIBS) $(LD_LIBS)
# Install directory - "make install" copies *.x executables there

If I have understood correctly, the problem is due to the MPI
library. Also, the pw_user_guide says "MPI libraries need to be
properly configured" (pw_user_guide-v6.4_page_20). But, why the
previous versions work fine and the problem occurred only on this
new released version v6.4? How this can be solved?

I will be happy to see any comments/suggestions from experts.

Thank you,
Hari Paudyal
SUNY-Binghamton


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--
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222



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diff --git a/Modules/Makefile b/Modules/Makefile
index 1970bed..438f210 100644
--- a/Modules/Makefile
+++ b/Modules/Makefile
@@ -160,7 +160,8 @@ ylmr2.o \
 wgauss.o \
 w0gauss.o \
 w1gauss.o \
-deviatoric.o
+deviatoric.o \
+read_upf.o   
 
 TLDEPS=libiotk libfox libutil libla libfft
 
diff --git a/Modules/make.depend b/Modules/make.depend
index db821b2..95457bd 100644
--- a/Modules/make.depend
+++ b/Modules/make.depend
@@ -320,10 +320,14 @@ read_pseudo.o : mp_images.o
 read_pseudo.o : pseudo_types.o
 read_pseudo.o : radial_grids.o
 read_pseudo.o : read_uspp.o
-read_pseudo.o : upf.o
 read_pseudo.o : upf_to_internal.o
 read_pseudo.o : uspp.o
 read_pseudo.o : wrappers.o
+read_upf.o : pseudo_types.o
+read_upf.o : radial_grids.o
+read_upf.o : read_upf_schema.o
+read_upf.o : read_upf_v1.o
+read_upf.o : read_upf_v2.o
 read_upf_schema.o : kind.o
 read_upf_schema.o : parser.o
 read_upf_schema.o : pseudo_types.o
diff --git a/Modules/qexsd.f90 b/Modules/qexsd.f90
index 07f68c8..35a76b5 100644
--- a/Modules/qexsd.f90
+++ b/Modules/qexsd.f90
@@ -707,13 +707,27 @@ CONTAINS
  CALL set_labels ()
  IF ( PRESENT(noncolin)) noncolin_ = noncolin 
  !
- IF (PRESENT(U))   CALL init_hubbard_commons(U, U_, label, 
"Hubbard_U") 
- IF (PRESENT(J0))  CALL init_hubbard_commons(J0, J0_, label, 
"Hubbard_J0" ) 
- IF (PRESENT(alpha)) CALL init_hubbard_commons(alpha, alpha_,label, 
"Hubbard_alpha") 
- IF (PRESENT(beta))  CALL init_hubbard_commons(beta, beta_, label, 
"Hubbard_beta")
- IF (PRESENT(J)) CALL init_hubbard_J (J, J_, label, "Hubbard_J" )
-

Re: [QE-users] (no subject)

[Pietro Davide Delugas]

Dear Yasmin

in the output there are these lines

DEPRECATED: no units specified in ATOMIC_POSITIONS card

and
Warning: card K_POINTS(AUTOMATIC) ignored
Warning: card  12 12 12 0 0 0 ignored

which seem to be unrelated to your input
could you check please. It would be also useful to have a look to the 
output of the scf calculation to understand what happened.

Pietro

On 03/19/2019 10:50 AM, yasmin kani wrote:
when i am running band structure for InSb. i have error "error opening 
xml data file". i attached my input and output file



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Re: [QE-users] Problem with tetrahedra method: from tetra_init : error # 26, cannot remap grid on k-point list

[Pietro Davide Delugas]

Dear Pacome

6.3 was released in July 2018 and in fact the new variable to dos.x was 
introduced only later in august


You can download 6.4 and use that one.
Pietro


On 03/17/2019 07:07 AM, Pacome NGUIMEYA wrote:

Dear Pietro,

I ran the scf calculation follows by the nscf calculation with
occupation='smearing', smearing and degauss (with QE-6.3.0).
I added  bz_sum = 'tetrahedra_opt' in the dos.x input file and I ran
it but, it crashed and I got the following error message

  task # 0
  from dos : error #19
  reading dos namelist

Apparently, the tetrahedron method is used if

  - "the input data file has been produced by pw.x using the
option
 occupations='tetrahedra', AND"
  - "a value for degauss is not given as input to namelist &dos"

read here https://gitlab.com/QEF/q-e/blob/qe-6.3/PP/Doc/INPUT_DOS.txt

But pw.x (nscf) does not work in my case

Further research on the internet led me to this website
https://eamonnmurray.gitlab.io/modelling_materials/lab04/ where I could
read that
  
"Essentially this corresponds to doing a three dimensional linear

interpolation from a regular grid of values."..."It’s important to note
that in a real measurement of the density of states of a system the
there is an implicit broadening that comes from

1. Electron-phonon coupling: the states are not simply at a fixed
energy, but will have some distribution as the atoms vibrate.

2. Any measurement probe will have a finite energy width associated
with it, which will limit how finely it can resolve density of states
features.

So while tetrahedron may seem the more accurate approach, you shouldn’t
necessarily think of it as a more correct representation of a real
system."

I think I am just going to use the common way, that is, running the
nscf calculation with smearing and degaus. Then, run this code

&DOS
prefix = '...',
outdir = '...',
fildos = 'dos.dat',
  /
and plot the DOS.

Regards - Pacome



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Re: [QE-users] pw_readschema_file failed retrieving input info from xml file ph.x using grid in qe-6.3-bkp and 2D cutoff

[Pietro Davide Delugas]

Hi

Thanks for reporting the issue.

As for the message about the missing input element, no problem it is the 
desired behavior, run_nscf started bby ph would not be able to fill 
correctly the
input element because the variable in input_parameters are not 
initialized, so the element is  not printed at all.


The isseus comes from the fact that in writing the status of the 2D 
cutoff we are currenlty using the value stored in input_parameters 
which, not being initialized, has in this case a wrong .false. value.


I will fix the issue in the develop, for further information check this 
issue on gitlab https://gitlab.com/QEF/q-e/issues/102


Pietro



On 03/11/2019 09:11 PM, Raphael Longuinhos Monteiro Lobato wrote:

Hi,

Using ph.x with grid may lead to

  Reading data from directory:
  scratch/X.Y/_ph0/test.save/
  Message from routine pw_readschema_file:
  failed retrieving input info from xml file, check it !!!

and wrong results.

In more details (sorry if not too methodical ... but I tried ... spent 
all day on it):


There is no problem with Gamma calculations ... as there is no bands 
to be read from /scratch/_ph0/ ... I guess.


Single-q, out Gamma (say X Y 0 instead 0. 0. 0.): tests without grid 
(without breaking in start_irr) in qe-6.3-bkp (3D), and in qe-5.1.1 
without/with grid leads to same results (as expected).


Using grid in qe-6.3-bkp (2D):

  + using only_init true leads to the message of error above ... the 
calculations goes on as if all were all right, and the frequencies are 
all wrong at the end (after collect).


  + using only_init true and reduce_io true (thus repeating the band 
structure calculations done at only_init calculations each time ... 
the xml is not saved in /scratch/_ph0/) leads to frequencies as 
expected when comparison to without grid calculations.


Using grid in qe-6.3-bkp (3D):
  + using only_init true leads to the expected results (comparison 
with previous 3D cases).


For me, it indicates it may be a problem when reading the information 
of 2D cutoff in the in /scrath/_ph0/test.save/data-file-schema.xml 
(same as /scrath/_ph0/test.xml).


The comparison between the scrathc/test.xml and /scratch/_ph0/test.xml 
when using the only_init true and reduce_io false shows indeed some 
unexpected discrepancies (e.g., from what I could get, it misses the 
fact that the scf was performed with assume isolated flag)


(note ... I use wf_collect false in the scf calculation and norm 
conserving pseudopotentials)


The above were single-q calculations. For the case of dispersion 
calculations using 2D, reading from /scratch/X.Y/test.save/ does not 
display the message. However, when reading the bands (reading from 
/scratch/X.Y/_ph0/test.q_X/test.save/data-file-schema.xml) it does 
display it (except for the 0. 0. 0. point ... in this case the bands 
are read from /scratch/test.save/ ) ... surprisingly, the calculations 
are correct ... I guess because in this case the code, somehow, does 
not miss the 2D flag, as it informs on the output of out.X.Y it is 
using 2D... the question remains "what is the information it misses 
when reading the bands from xml ... and when it will lead to error on 
the results ? "


Also, a previous post 
http://lists.quantum-espresso.org/pipermail/users/2018-October/041419.html
... the celldm problem in the dyn header remains in 6.3-backports ... 
and one have to correct it by hand on the .dyn


If these are indeed unexpected error (not my ...  if someone can 
reproduce it) yet not solved (sorry if I miss the solution in older 
posts), the real problem is ... I don't have idea to help solving them 
...  although I could give it a try with some guide.


best,



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