Re: [QE-users] Inability of QE compiled for GPUs to read SG15 ONCV Potentials

[Paolo Giannozzi]

Can't reproduce your problem (nvfortran v.22.7).


end of file reached, tag PP_HEADER not found


PP_HEADER is the first tag that is actually read. It looks like there 
are spurious characters in the file, like CRLF.


Paolo



  end of file reached, tag not found

  end of file reached, tag PP_MESH not found

  end of file reached, closing tag not found

…

01


%%

Error in routine set_dft_from_name (2):

conflicting values for iexch

%%


The Pseudopotentials are obtained from 
http://www.quantum-simulation.org/potentials/sg15_oncv/ 
<http://www.quantum-simulation.org/potentials/sg15_oncv/>



I see it for both scalar relativistic and fully relativistic pseudo 
potentials. The specific pseudpotentials for which it failed are


Br_ONCV_PBE-1.2.upf

Br_ONCV_PBE_FR-1.0.upf


Could you please let me know if you have any idea why? I will be happy 
to share the build info if you need it.



Thanks,

Soham Ghosh

HPC performance engineer,

NERSC at LBL


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Re: [QE-users] Issue Compiling QE 7.3 on MacOS 14.4.1

[Paolo Giannozzi]

On 25/04/2024 21:41, Paolo Giannozzi wrote:

3. Check that __GPU is not set as a preprocessing variable 


"__CUDA", not "__GPU"

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Re: [QE-users] Issue Compiling QE 7.3 on MacOS 14.4.1

[Paolo Giannozzi]

1. Look at the line that performs the link, verify that libupf.a and 
libks.a follow libpw.a (they should)
2. Verify whether the missing symbols have been properly compiled. For 
instance: delete upflib/ylmr2_gpu.o, recompile, look carefully for any 
compilation error
3. Check that __GPU is not set as a preprocessing variable (none of the 
missing routine should do anything in your setting, they are stubs)


Paolo

On 25/04/2024 20:15, Robert Fleming via users wrote:
I have been a QE user since v7.1; I skipped v7.2 on my local machine, 
and am now trying to compile 7.3.  I’m running into a compilation error 
that I don’t quite know what to do about:


The configure script completes successfully with all expected compilers 
and libraries detected.  However, I’m getting an error for undefined 
symbols for the x86_64 architecture for ld (I’m using an Intel i9).


Any guidance on how to address this?

ld: warning: -commons use_dylibs is no longer supported, using error 
treatment instead


Undefined symbols for architecture x86_64:

   "_ccgdiagg_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_init_us_2_base_gpu_", referenced from:

       ___uspp_init_MOD_init_us_2 in libpw.a(init_us_2.o)

   "_pcegterg_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_ppcg_gamma_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_ppcg_k_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_pregterg_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_rcgdiagg_gpu_", referenced from:

       _diag_bands_ in libpw.a(c_bands.o)

   "_rotate_wfc_gamma_gpu_", referenced from:

       _rotate_wfc_gpu_ in libpw.a(rotate_wfc_gpu.o)

   "_rotate_wfc_k_gpu_", referenced from:

       _rotate_wfc_gpu_ in libpw.a(rotate_wfc_gpu.o)

   "_ylmr2_gpu_", referenced from:

       _atomic_wfc_gpu_ in libpw.a(atomic_wfc_gpu.o)

ld: symbol(s) not found for architecture x86_64

collect2: error: ld returned 1 exit status

make[2]: *** [pw.x] Error 1

make[1]: *** [pw] Error 1

make: *** [pw] Error 1



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] QE as a library

[Paolo Giannozzi]

On 23/04/2024 10:10, Alireza Ghasemi wrote:

   Can QE be called as a library? For example, a small program that 
provides a structure to a QE routine and the routine returns energy and 
forces, or possibly more than these two quantities?
it can, sort of. There are routines that perform a specific task, but 
they typically need quite a bit of initialization to work. It depends a 
lot upon what you want to achieve and which level of granularity in 
calling QE routines you need, or desire


Paolo
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Re: [QE-users] A strange error when using GPU accelerated ph.x

[Paolo Giannozzi]

I am not sure that the electron-phonon calculations are available for 
GPU eecution in the QE version you are running. In any event you should 
provide your data so that one can figure out whether your problem is 
reproducible or not


Paolo

On 4/19/24 18:00, lq1998 via users wrote:

Dear developers and users,

I tried to run GPU version of QE for electron phonon coupling 
calculation on an a100 card. The structure relaxation and 
self-consistent calculation are successful. However, when I did phonon 
calculation, my job crashed with a strange error:


##
[m005:65520:0:65520] Caught signal 11 (Segmentation fault: address not 
mapped to object at address 0xfffc)


/fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phq_setup.f90: [ phq_setup_() ]
       ...
       322   !     nat_todo, atomo, comp_irr
       323
       324   DO irr=0,nirr
==>   325      comp_irr(irr)=comp_irr_iq(irr,current_iq)
       326      IF (elph .AND. irr>0) comp_elph(irr)=comp_irr(irr)
       327   ENDDO
       328   !

 backtrace (tid:  65520) 
  0 0x004a2780 phq_setup_()  
/fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phq_setup.f90:325
  1 0x004700e1 initialize_ph_()  
/fs08/home/js_luqing/src/qe-7.2/PHonon/PH/initialize_ph.f90:79
  2 0x0041a811 do_phonon_()  
/fs08/home/js_luqing/src/qe-7.2/PHonon/PH/do_phonon.f90:100
  3 0x00413d25 MAIN_()  
/fs08/home/js_luqing/src/qe-7.2/PHonon/PH/phonon.f90:78

  4 0x00413c71 main()  ???:0
  5 0x00022555 __libc_start_main()  ???:0
  6 0x0040cd8d _start()  ???:0
=
[m005:65520] *** Process received signal ***
[m005:65520] Signal: Segmentation fault (11)
[m005:65520] Signal code:  (-6)
[m005:65520] Failing at address: 0x6a8fff0
[m005:65520] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2ac4edf09630]
[m005:65520] [ 1] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x4a2780]
[m005:65520] [ 2] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x4700e1]
[m005:65520] [ 3] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x41a811]
[m005:65520] [ 4] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x413d25]
[m005:65520] [ 5] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x413c71]
[m005:65520] [ 6] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2ac4ee9e7555]
[m005:65520] [ 7] /fs08/home/js_luqing/src/qe-7.2/bin/ph.x[0x40cd8d]
[m005:65520] *** End of error message ***
--
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--
--
mpirun noticed that process rank 0 with PID 0 on node m005 exited on 
signal 11 (Segmentation fault).

#

I am not an expert of coding, but it seems like the line 325 wasn't 
recognized, which is fairly strange. I don't know how to solve this 
problem, and I am glad if anyone can help me.


Yours,
Qing Lu


lq1998
1148330...@qq.com

<https://wx.mail.qq.com/home/index?t=readmail_businesscard_midpage=true=lq1998=http%3A%2F%2Fthirdqq.qlogo.cn%2Fg%3Fb%3Doidb%26k%3DnAlU7tDw3a3nocdsLBEZ0w%26kti%3DZSIdLwA%26s%3D640%26t%3D1608227631=1148330678%40qq.com=vu-r6llqRDfPnVFzvkV9IDNZDyJF2SqLzDMX6V3ESnRliznjLXDgHW0qv6MBvKBkTl_-0re_DZnkyIqf97_KKw>

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Re: [QE-users] Difference between data file saved inside outdir

[Paolo Giannozzi]

hdf5 files are in portable format, one per k-point, independent upon the 
number of processors and the kind of parallelization.


prefix.wfc* files are in nonportable binary format, one per processor, 
depend upon the number of processors and the kind of parallelization.


For reasons that is too long to explain, calculations that use SCF 
wavefunctions read then from "portable" format and re-write them to 
"non-portable" format. It's a little bit dumb and actually unnecessary 
in most cases.


Paolo

On 28/03/2024 08:04, Abdul Muhaymin via users wrote:

Hello all,

After a spin-polarized scf calculation, I have several files such as 
wfcup#.hdf5, wfcdw#hdf5 etc in in outdir/prefix.save. The number of the 
files are equal to the 2*number of k points. However, after nscf 
calculation, I am getting more data files in the outdir (not in 
outdir/prefix.save). I have N number of prefix.wfc* files where N is the 
number of processor I used. What is the difference between these two 
type of files? Are they both wavefunction? If I delete them, will there 
be any problem?


Sincerely,
Abdul Muhaymin,
Graduate student,
Bilkent University, Ankara.
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Re: [QE-users] lambda.x: at line 61 of file lambda.f90

[Paolo Giannozzi]

On 19/04/2024 10:21, Dawid Ciszewski wrote:


At line 61 of file lambda.f90 (unit = 5, file = 'stdin')
Fortran runtime error: End of file


look at line 61 of file lambda.f90: it reads the first line of the 
input. You are not reading the input file.


Paolo
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Re: [QE-users] QE 7.2 error required attribute rank not found

[Paolo Giannozzi]

Can't reproduce

Paolo

On 12/04/2024 09:43, Sol Loja via users wrote:

Dear QE Users Forum,

I am encountering the following error after running a nscf calculation 
on QE 7.2:


  %%
      task #         0
      from qes_read: matrixType : error #        10
      required attribute rank not found, can't read further, stopping
  %%


Please advise me on how to address this. Below is the input file:


ibrav=1,
celldm(1)=15,
nat=3,
ntyp=2,
ecutwfc=44.099,
ecutrho=440.99,
/

conv_thr=1.0d-6,
mixing_beta=0.7,
/

ion_dynamics = 'bfgs',
/
ATOMIC_SPECIES
C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF
O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
C             7.50        7.50        7.50    0  
  0   0

O             8.6736893489        7.5000297668        7.5000297668
O             6.3262902178        7.4999803011        7.4999803011
K_POINTS {gamma}

Best regards,
Sol Loja

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Re: [QE-users] [SPAM] about relax-structure issue

[Paolo Giannozzi]

On 18/04/2024 15:14, 孙昊冉 wrote:


Dear Professors and Experts:


When I use pw.x to relax a cell structure. I meet a question that "= Bad 
termination of one of your application processes =rank 0 pid... running 
at ...  =exit status: 3." I wonder that what is the exactly meaning of 
exit status: 3.


it means that the ionic optimization has not converged (see the header 
of PW/src/run_pwscf.f90). You should look at the output for more information


Paolo


Many Thanks

The input file is list as follows:



   calculation='vc-relax'

   disk_io='low'

   prefix='***'

   restart_mode='from_scratch'

   verbosity='high'

   tprnfor=.true.

   tstress=.true.

   pseudo_dir = '~/qe-6.8/pseudo'

   forc_conv_thr=1.0d-5

   outdir='./tmp'

/



   ibrav= 0,

   nat= 40,

   ntyp= 2,

   occupations = 'smearing', smearing = 'gauss', degauss = 1.0d-2,

   ecutwfc = 160,

   ecutrho = 800,

/



   conv_thr = 1.0d-8

   mixing_beta = 0.7d0

   diagonalization = 'cg'

/



     ion_dynamics='bfgs'

/



     press_conv_thr=0.1

/

ATOMIC_SPECIES

  ***

CELL_PARAMETERS (angstrom)

   ***

ATOMIC_POSITIONS (crystal)

  ***

K_POINTS {automatic}

***



Dr Haoran

Xinjiang University, Urumqi

18/4/2024






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Re: [QE-users] [SPAM] outRelax001.txt

[Paolo Giannozzi]

I confirm: it runs on 2 nodes with 4 GPUs (of a big machine)

Paolo

On 17/04/2024 16:45, Paolo Giannozzi wrote:

I think it is just a problem of memory: it's a rather big job

Paolo

PS: 'dft-d3' or 'DFT-D3', 'dft-D3' is not recognized (note the warning 
in the output)


On 17/04/2024 11:20, Vor st via users wrote:

Dear users and developers,

   calculation = 'relax'
   etot_conv_thr =   6.00d-05
   forc_conv_thr =   1.00d-04
   outdir = './out/'
   prefix = 'aiida'
   pseudo_dir = './pseudo/'
   tprnfor = .true.
   tstress = .true.
   verbosity = 'high'
   tprnfor = .true.
   tstress = .true.
   verbosity = 'high'
   tefield       = .true.
   dipfield      = .true.
   wf_collect = .true.
   !max_seconds = 64800
/

   degauss =   0.02
   ecutrho =   5.00d+02
   ecutwfc =   5.00d+01
   ibrav = 0
   nat = 192
   !nosym = .true.
   !nspin = 2
   ntyp = 2
   occupations = 'smearing'
   smearing = 'gaussian'
   vdw_corr = 'dft-D3'
   edir        = 3
   emaxpos     = 0.85
   eopreg      = 0.0357419858
   eamp        = 0.0
/

   !conv_thr =   1.20d-09
   electron_maxstep = 300
   mixing_beta =   4.00d-01
/

/

/
ATOMIC_SPECIES
O      15.9994 O.pbesol-n-kjpaw_psl.0.1.UPF
Ti     47.867 ti_pbesol_v1.4.uspp.F.UPF
ATOMIC_POSITIONS crystal
O    0.00    0.00    0.00    0    0    0
O    0.00    0.25    0.00    0    0    0
O    0.00    0.50    0.00    0    0    0
O    0.00    0.75    0.00    0    0    0
O    0.25    0.00    0.00    0    0    0
O    0.25    0.25    0.00    0    0    0
O    0.25    0.50    0.00    0    0    0
O    0.25    0.75    0.00    0    0    0
O    0.50    0.00    0.00    0    0    0
O    0.50    0.25    0.00    0    0    0
O    0.50    0.50    0.00    0    0    0
O    0.50    0.75    0.00    0    0    0
O    0.75    0.00    0.00    0    0    0
O    0.75    0.25    0.00    0    0    0
O    0.75    0.50    0.00    0    0    0
O    0.75    0.75    0.00    0    0    0
Ti    0.875000    0.00    0.014514    0    0    0
Ti    0.875000    0.25    0.014514    0    0    0
Ti    0.875000    0.50    0.014514    0    0    0
Ti    0.875000    0.75    0.014514    0    0    0
Ti    0.125000    0.00    0.014514    0    0    0
Ti    0.125000    0.25    0.014514    0    0    0
Ti    0.125000    0.50    0.014514    0    0    0
Ti    0.125000    0.75    0.014514    0    0    0
Ti    0.375000    0.00    0.014514    0    0    0
Ti    0.375000    0.25    0.014514    0    0    0
Ti    0.375000    0.50    0.014514    0    0    0
Ti    0.375000    0.75    0.014514    0    0    0
Ti    0.625000    0.00    0.014514    0    0    0
Ti    0.625000    0.25    0.014514    0    0    0
Ti    0.625000    0.50    0.014514    0    0    0
Ti    0.625000    0.75    0.014514    0    0    0
O    0.125000    0.125000    0.029028    0    0    0
O    0.125000    0.375000    0.029028    0    0    0
O    0.125000    0.625000    0.029028    0    0    0
O    0.125000    0.875000    0.029028    0    0    0
O    0.375000    0.125000    0.029028    0    0    0
O    0.375000    0.375000    0.029028    0    0    0
O    0.375000    0.625000    0.029028    0    0    0
O    0.375000    0.875000    0.029028    0    0    0
O    0.625000    0.125000    0.029028    0    0    0
O    0.625000    0.375000    0.029028    0    0    0
O    0.625000    0.625000    0.029028    0    0    0
O    0.625000    0.875000    0.029028    0    0    0
O    0.875000    0.125000    0.029028    0    0    0
O    0.875000    0.375000    0.029028    0    0    0
O    0.875000    0.625000    0.029028    0    0    0
O    0.875000    0.875000    0.029028    0    0    0
O    0.875000    0.00    0.085377    0    0    0
O    0.875000    0.25    0.085377    0    0    0
O    0.875000    0.50    0.085377    0    0    0
O    0.875000    0.75    0.085377    0    0    0
O    0.125000    0.00    0.085377    0    0    0
O    0.125000    0.25    0.085377    0    0    0
O    0.125000    0.50    0.085377    0    0    0
O    0.125000    0.75    0.085377    0    0    0
O    0.375000    0.00

Re: [QE-users] [SPAM] outRelax001.txt

[Paolo Giannozzi]

 cooperation amongst peoples
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Re: [QE-users] calculated number of k_points calculated different than instructed in the nscf input file

[Paolo Giannozzi]

A 'nscf' calculation assumes that the k-point grid covers the 
Irreducible Brillouin Zone computed with the crystal symmetry. If your 
grid covers the IBZ computed for a higher symmetry, the missing k-points 
will be added. Use calculation='bands' or disable the symmetry check on 
k-points if you want to stick to the k-point grid you provided


Paolo

On 17/04/2024 06:13, wenusaras wrote:


After a scf calculation, I performed a nscf calculation using a 10 10 1
grid.

K_POINTS {crystal}
100
   0.  0.  0.  1.00e-02
   0.  0.1000  0.  1.00e-02
   0.  0.2000  0.  1.00e-02
...
   0.9000  0.9000  0.  1.00e-02

Though the nscf input file is instructed to do so, the nscf.out files
calculates for 247 kpoints.

  number of k points=   247  Marzari-Vanderbilt smearing, width (Ry)=
  0.0150
    cart. coord. in units 2pi/alat
     k(    1) = (   0.000   0.000   0.000), wk =
0.020
     k(    2) = (   0.000   0.1154701   0.000), wk =
0.007
     k(    3) = (   0.000   0.2309401   0.000), wk =
0.007
...
     k(  247) = (   1.800  -0.900   0.000), wk =
0.007


Could you please let me know why this happens and how could I calculates
for 100 kpoints as instructed in nscf.in?


--
Thank You
Wenusara Satheekshana

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Re: [QE-users] libgomp: TODO error while running pw.x

[Paolo Giannozzi]

On 4/14/24 15:25, Bhargab Kakati wrote:



mpirun -np 8 /home/cmsgpu/softwares/qe-7.3-no-openmp/qe-7.3/bin/pw.x
 Fe.scf.out | tee error.txt


you should look into the output (Fe.scf.out) in order to figure out the 
"true" error. The lines below do not contain any useful information


Paolo



libgomp: TODO

libgomp: TODO

libgomp: TODO

libgomp: TODO

libgomp: TODO

libgomp: TODO

libgomp: TODO

libgomp: TODO
--
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--
--
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:

   Process name: [[32487,1],7]
   Exit code:    1


my system configuration is:

OS: Ubuntu 22.04
CPU: 36 Core
GPU: Nvidia RTX A6000
CUDA Version: 12.3

nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Fri_Nov__3_17:16:49_PDT_2023
Cuda compilation tools, release 12.3, V12.3.103
Build cuda_12.3.r12.3/compiler.33492891_0

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Re: [QE-users] QE GPU ORTE_ERROR problem

[Paolo Giannozzi]

On 4/11/24 20:45, Sitangshu Bhattacharya wrote:


*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***and potentially your MPI job)


Occasionally I also encounter this problem: there is some mismatch 
between the MPI libraries linked by the compiler and those loaded at 
run-time. Ensure that your NVidia HPC SDK is properly set up, that 
environment variables have the correct value, that the mpif90 you are 
using is the one in the NVidia HPC SDK and not something else, same for 
MPI libraries, ...


Paolo


[login02:158963] Local abort before MPI_INIT completed completed 
successfully, but am not able to aggregate error messages, and not able 
to guarantee that all other processes were killed!



Any solutions?


Regards,

**
Sitangshu Bhattacharya (সিতাংশু ভট্টাচার্য), Ph.D
Assistant Professor,
Room No. 2221, CC-1,
Electronic Structure Theory Group,
Department of Electronics and Communication Engineering,
Indian Institute of Information Technology-Allahabad
Uttar Pradesh 211 012
India
Telephone: 91-532-2922000 Extn.: 2131
Web-page: http://profile.iiita.ac.in/sitangshu/ 
<http://profile.iiita.ac.in/sitangshu/>

Institute: http://www.iiita.ac.in/ <http://www.iiita.ac.in/>


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Re: [QE-users] Output of post-processing pp.x for 1D plot of the pseudo charge density from individual orbitals

[Paolo Giannozzi]

The third column is the integral of the second one along the chosen 
path. It is useful for the radially averaged charge density. Don't know 
about the negative sign: it might be an artifact of the interpolation, 
or, for ultrasoft pseudopotentials, a case of "negative charge"


Paolo

On 15/04/2024 11:56, Marin Luca wrote:


Dear QE users,


I'm facing difficulties in interpreting the output of pp.x. I'm running 
a scf calculation on an isolated atom of Xe and a subsequent 
post-processing in order to plot the (pseudo) charge density coming from 
the individual atomic orbitals. I am running QE v6.4.1


By reading the manual of pp.x (PP/Doc/INPUT_PP.txt), I read that it 
should be possible to obtain a 1D plot (a simple x-y plot of a 1D 
function) of this charge density. I tried to do so with the following 
input file:




prefix = 'smoothy',
outdir = './smoothy/',
filplot = 'smoothy.dat',
plot_num = 7,
kpoint=1,
kband(1) = 1,
kband(2) = 18,
!lsign=.true.
/

filepp(1)= 'smoothy.dat'
weight(1) = 1.0

iflag=0
output_format = 0,

fileout = 'smoothy.plt'
e1(1) = 0.5,
e1(2) = 0.5,
e1(3) = 0.5,
x0(1) = 0,
x0(2) = 0,
x0(3) = 0,
nx = 800
/

in which my idea is to plot the charge density of each orbital along 
that line defined by the vectors e1 and x0.


The calculation finishes fine, but the output "plottable" files contain 
3 columns (they look like this):


         0.00       -0.0174697150        0.00
         0.0012515645       -0.0174697013       -0.07
         0.0025031289       -0.0174696330       -0.36
         0.0037546934       -0.0174694282       -0.000101
         0.0050062578       -0.0174689508       -0.000216

and many other lines. While I sort of get that the first column is the 
spatial variable and the second should be the charge density (the 
|\psi|^2), I have no clue what the third column is.


Could anyone explain to me what the third column means and what I should 
plot in order to get the pseudo charge density as a function of this 
radial coordinate only? Moreover, even with lsign commented out, some 
values of the second column are negative which is very weird as this 
should be |\psi|^2. Do you also have an answer on this?


I thank you all in advance for your help and time!

Best wishes,
Luca

ETH Zurich
Luca Marin
Materials Theory
Department of Materials
HIT G 43.1
Wolfgang-Pauli-Strasse 27
8093 Zurich, Switzerland
phone +41 44 633 81 67
luca.ma...@mat.ethz.ch <mailto:luca.ma...@mat.ethz.ch>
https://www.theory.mat.ethz.ch <https://www.theory.mat.ethz.ch/>


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Re: [QE-users] Restart in hybrid HSE calculation

[Paolo Giannozzi]

bpthread-2.28.s  154BDCF0  Unknown               Unknown  Unknown



Please write if possible:
1) use the obtained result (for example, charge-density.dat) to run the 
same calculation? How to do this and will it help to perform the 
calculation with the same resources (140 cores, 5 TB RAM)?
2) simplify the input file to speed up the calculation (or reduce the 
required resources)


Thanks in advance,
Alex



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Re: [QE-users] Problem related to initiate EPW

[Paolo Giannozzi]

On 4/5/24 07:00, 胡大展 wrote:


But there is no gcc640 & openmpi-1.10.7 in my HPC:


You do not need that specific version of the compiler and of OpenMP.
The list you report is old and suitable for an old code version. If you 
plan to use a recent version of the code, you may use any recent version 
of GCC or Intel and OpenMPI. Same if you want to use the old code 
version instead, but you should maybe avoid the most recent compiler 
releases.


Paolo
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Re: [QE-users] [SPAM] nscf calculation error

[Paolo Giannozzi]

I am afraid (for you) that the origin of your problem is in your 
compiler. There is nothing wrong in your xml file: it looks exactly like 
the one that I generate and subsequently read


Paolo
On 3/25/24 09:33, Максим Кузнецов wrote:

25.03.2024, 11:02, "Paolo Giannozzi" :

I don't see how what you describe may happen, unless:
- you are reading data files produced by earlier code versions, or
- you are using some exotic, little-tested option.
Please provide the input data and maybe also the xml data produced in
the scf run

Paolo

On 3/24/24 19:30, Максим Кузнецов wrote:


  Dear users,
  I encountered the following problem:
  sсf calculation works correctly, but when I try to run nscf
calculation
  I get the following error:
     Atomic positions and unit cell read from directory:
        ./out/KFeS2.save/
        Message from routine qes_read:symmetriesType:
        error reading nsym
    
%%
        Error in routine qes_read: matrixType (10):
        required attribute rank not found, can't read further,
stopping
    
%%
  However all tests in test-suite passed.
  QE version 7.3.1
  I'll be very grateful for reply!



  Sincerely,
  Kuznetsov Maksim,
  Masters student,
  Kazan Federal University.

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

  Sincerely,
  Kuznetsov Maksim,
  Masters student,
  Kazan Federal University.


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Re: [QE-users] [SPAM] nscf calculation error

[Paolo Giannozzi]

I don't see how what you describe may happen, unless:
- you are reading data files produced by earlier code versions, or
- you are using some exotic, little-tested option.
Please provide the input data and maybe also the xml data produced in 
the scf run


Paolo

On 3/24/24 19:30, Максим Кузнецов wrote:


Dear users,
I encountered the following problem:
sсf calculation works correctly, but when I try to run nscf calculation 
I get the following error:

   Atomic positions and unit cell read from directory:
      ./out/KFeS2.save/
      Message from routine qes_read:symmetriesType:
      error reading nsym
  %%
      Error in routine qes_read: matrixType (10):
      required attribute rank not found, can't read further, stopping
  %%
However all tests in test-suite passed.
QE version 7.3.1
I'll be very grateful for reply!

  


Sincerely,
Kuznetsov Maksim,
Masters student,
Kazan Federal University.



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Re: [QE-users] Too few bands

[Paolo Giannozzi]

On 3/22/24 13:05, aleksandr.doma--- via users wrote:

3) /"wf_collect I think is no longer used" /-- I'd like to use LOBSTER 
analysis... so maybe it will be necessary.


no: it has no effect at all

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Re: [QE-users] Phonon calculations with different parallelization

[Paolo Giannozzi]

On 3/21/24 11:03, Chirantan Pramanik wrote:


The phonon frequencies are not the same


basically, they are. The differences are small (a few cm-1 at most) and 
mostly affect low-lying frequencies. Self-consistency is not very tight 
(1E-14) and may already explain the observed differences.


Paolo


Regards,
Chirantan


*From:* Paolo Giannozzi 
*Sent:* Thursday, March 21, 2024 11:34 AM
*To:* Quantum ESPRESSO users Forum ; 
Chirantan Pramanik 
*Subject:* Re: [QE-users] Phonon calculations with different 
parallelization

On 3/21/24 03:45, Chirantan Pramanik wrote:


My Phonon calculations provide different frequency values for different 
parallelization on the cluster especially for the total number of 
processors used. Is itpossible or I am doing something very wrong? As 
vibrational frequency is gauge invariat how it can be possible?


Thanks,
Chirantan


It is not possible, with one exception: zero-frequency acoustic modes
that have non-zero frequencies; these can vary a lot, but they are
anyway set to zero by imposing the acoustic sum rule.

It might be a bug, but it is hard to say more without knowing what you
exactly computed on which code version

Paolo
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216


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Re: [QE-users] Phonon calculations with different parallelization

[Paolo Giannozzi]

On 3/21/24 03:45, Chirantan Pramanik wrote:


My Phonon calculations provide different frequency values for different 
parallelization on the cluster especially for the total number of 
processors used. Is itpossible or I am doing something very wrong? As 
vibrational frequency is gauge invariat how it can be possible?


Thanks,
Chirantan


It is not possible, with one exception: zero-frequency acoustic modes 
that have non-zero frequencies; these can vary a lot, but they are 
anyway set to zero by imposing the acoustic sum rule.


It might be a bug, but it is hard to say more without knowing what you 
exactly computed on which code version


Paolo
--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] error in produce pseudopotentials

[Paolo Giannozzi]

On 3/19/24 13:35, wangzongyi via users wrote:

.../public3/home/scg9084/wzy/qe-7.2-new/bin/ld1.x: error while loading 
shared libraries: libmkl_intel_lp64.so: cannot open shared object file: 
No such file or directory


I can't understand what it means


it means that you haven't correctly set the envuribmental variables 
(LIBRAARY_PATH, LD_LIBRARY_PATH) needed to use the Intel MKL libraries. 
It is a problem of your system configuration, not of QE.


Paolo
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Re: [QE-users] ibrave=-12

[Paolo Giannozzi]

On 16/03/2024 11:49, Fariba Nazari via users wrote:

​Dear all,

Does crystal_b work for ibrave=-12?


for "ibrave"=-12, no. For "ibrav"=-12, it should work

Paolo


Best Regards
Fariba Nazari
IASBS

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[QE-users] Fwd: Problem with electric polarization calculation in quantum espresso

[Paolo Giannozzi]

(large attachment removed, the pseudopotential file is 
Bi.pbe-dn-rrkjus_psl.0.2.2.UPF)

 Forwarded Message 
Subject:Problem with electric polarization calculation in quantum 
espresso
Date:   Thu, 14 Mar 2024 01:05:32 +
From:   Akshay Mahajan 
To: users@lists.quantum-espresso.org 


Dear QE Users,
I have been trying to calculate electric polarization for a 2D Bi 
monolayer (along the in-plane x-direction). I am using QE version 
6.4.1.There are two issues that I am facing,


 1.
The magnitude of the polarization changes significantly when the k_y
values change (I am keeping k_z to 1 only since it is a 2D system).
I expected it to reach some converged value but rather it keeps
increasing on increasing the k_y value and then drops and then again
starts increasing. The bash file is included in the email for this
calculation. In the bash file (polarization_conv.sh) I am changing
both k_x and k_y in the scf calculation and changing nppstr to 2*k_x
and keeping k_x =nppstr in the nscf calculation. The result from
running this bash script run is also included(pol_conv_Bi_mono). One
can modify the script and check that only changing the k_y is
causing this huge change in the polarization values.
 2.
As per this paper
(https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.201707383
)
the positive delta_h (refer to the paper for definition) should
result in a positive polarization. While trying to calculate the
variation of electric polarization with delta_h, I am getting
negative polarization values for positive delta_h near the
centrosymmetric structure (delta_h=0) and positive values for
negative delta_h (again near the centrosymmetric structure
(delta_h=0)). The bash script (polarization.sh) for this calculation
and the result(pol_data_Bi_mono) are also attached.

I am also attaching the pseudopotential file for reference. Please let 
me know if anyone can determine the issue behind these incorrect results.

Thank you.
Regards,
*Akshay Mahajan*
*Ph.D. Student *
*Prime Minister Research Fellow (PMRF) *
*Solid State and Structural Chemistry Unit (SSCU) *
*Indian Institute of Science (IISc)*
*Bengaluru, India *

pol_conv_Bi_mono
Description: Binary data


pol_data_Bi_mono
Description: Binary data
#!/bin/bash

# Script to get the energy versus polarization and energy versus displacement plots
# Exclusive for Bi project (uses verticle dispalcement for polarization)

# Energy conversion from Ry to eV parameter #
Q=13.605703976
# Intial values from relaxed FE structure #
h_u_pol=18.419321249 # polar h displacement in upper layer
h_l_pol=15.420625873 # polar h displacement in lower layer
u_ref=17.790480876   # ref for polar h displacement in upper layer
l_ref=14.791753001   # ref for polar h displacement in lower layer
z_vacc=33.211090088  # Lattice parameter along the vaccum

# Initializing the delta_h values for polar structure #
delta_h_u_pol=`echo "scale=9; $h_u_pol - $u_ref" | bc`
delta_h_l_pol=`echo "scale=9; $h_l_pol - $l_ref" | bc`

# Initializing the delta_h value of equally stable other polar structure #
neg=-1
neg_delta_h_u_pol=`echo "scale=9; $delta_h_u_pol * $neg" | bc`
neg_delta_h_l_pol=`echo "scale=9; $delta_h_l_pol * $neg" | bc`

# Intializing the outskirt of polar displacement for plotting W curves #
## positive outskirt
#u_pos_max=`echo "scale=9; 2.5*$delta_h_u_pol" | bc`
#l_pos_max=`echo "scale=9; 2.5*$delta_h_l_pol" | bc`
## negative outskirt
#u_neg_max=`echo "scale=9; 2.5*$neg_delta_h_u_pol" | bc`
#l_neg_max=`echo "scale=9; 2.5*$neg_delta_h_l_pol" | bc`

# Creating delta_h values for upper layer #
#delta_h_u_list=($(seq $u_pos_max -0.15 $delta_h_u_pol))
#delta_h_u_list+=($(seq $delta_h_u_pol -0.05 0))
delta_u=`echo "scale=9; $delta_h_u_pol/10" | bc`
delta_u_lst=`echo "scale=9; $delta_u * $neg" | bc`
delta_h_u_list=($(seq $delta_h_u_pol $delta_u_lst 0))
## getting the negative displacements
u_neg_delta_list=()
for (( idx=${#delta_h_u_list[@]}-1 ; idx>=0 ; idx-- )); do
u_neg_delta_list+=(`echo "scale=9; ${delta_h_u_list[$idx]} * $neg" | bc`)
done
## appending the negative displacements
delta_h_u_list+=(0)
delta_h_u_list+=(${u_neg_delta_list[@]})

# Creating delta_h values for lower layer # 
#delta_h_l_list=($(seq $l_pos_max -0.15 $delta_h_l_pol))
#delta_h_l_list+=($(seq $delta_h_l_pol -0.05 0))
delta_l=`echo "scale=9; $delta_h_l_pol/10" | bc`
delta_l_lst=`echo "scale=9; $delta_l * $neg" | bc`
delta_h_l_list=($(seq $delta_h_l_pol $delta_l_lst 0))
## getting the negative displacements
l_neg_delta_list=()
for (( idx=${#delta_h_l_list[@]}-1 ; idx>=0 ; idx-- )); do
l_neg_delta_list+=(`echo "scale=9; ${delta_h_l_list[$idx]} * $neg" | bc`)
done
## appending the negative dispalcements

Re: [QE-users] puzzle on homo higher than lumo

[Paolo Giannozzi]

If you set occupancies to "fixed", the code assumes that the system is 
an insulator and computes the HOMO as the highest N-th Kohn-Sham state, 
the LUMO as the lowest (N+1)-th KS state (N=half the number of 
electrons). If the system does not want to be an insulator, the "HOMO" 
might turn out to have higher energy than the "LUMO".


Paolo

On 09/03/2024 03:38, wangzongyi via users wrote:

Dear all
I am trying to calculate metallic oxide(CoO). However, I have some 
puzzle in writing vcrelax.in file.
As the experience shows that CoO is insulator, my vcrelax.in file is 
showed in the following lines, I calculate it as insulator

* *
*    calculation='vc-relax'*
*    restart_mode='from_scratch',*
*    prefix='CoO'*
*    pseudo_dir = '../../files/pseudo'*
*    outdir='./tmp'*
*    verbosity='high'*
*    etot_conv_thr = 1.0D-4*
*    forc_conv_thr = 1.0D-3*
* /*
* *
*    ibrav = 0,*
*    celldm(1) = 8.00,*
*    nat = 4,*
*    ntyp = 3,*
*    ecutwfc = 50.0*
*    ecutrho = 400.0*
*    nspin = 2*
*    tot_magnetization=0.00*
*    occupations = 'fixed',*
*    nbnd = 28*
* /*
* *
*    conv_thr =  1.d-10*
*    startingwfc ='file'*
*    startingpot ='file'*
* /*
* *
*    ion_dynamics = 'bfgs'*
* /*
* *
*    cell_dynamics = 'bfgs'*
* /*
*ATOMIC_SPECIES*
* Co1  58.933194  co_pbesol_v1.2.uspp.F.UPF*
* Co2  58.933194  co_pbesol_v1.2.uspp.F.UPF*
* O    15.999     O.pbesol-n-kjpaw_psl.0.1.UPF*
*ATOMIC_POSITIONS {crystal}*
*Co1      0.     0.     0.*
*Co2      0.5000     0.5000     0.5000*
*O        0.2500     0.2500     0.2500*
*O        0.7500     0.7500     0.7500*
*CELL_PARAMETERS {alat}*
*   0.570726115   0.570726115   1.031099100*
*   0.570726115   1.031099100   0.570726115*
*   1.031099100   0.570726115   0.570726115*
*K_POINTS {automatic}*
* 6 6 6 0 0 0*
*HUBBARD {ortho-atomic}*
*U Co1-3d  6.7553*
*U Co2-3d  6.7553*
however, the outfile shows that
*highest occupied, lowest unoccupied level (ev):    14.3247   13.7975*
I am puzzled, what happened, why is homo higher than lumo? is my 
calculation correect? Or should I regard the system as matel when 
calculate varelax?

Thank you very much

--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] [Phonopy error] "Parsing "scf-001.out" failed"

[Paolo Giannozzi]

I guess you should inquire with the developers of PhonoPy, not here. 
Before doing that, note that forces are not present in *out files. This 
does not look right to me.


Paolo

On 01/03/2024 07:05, 임용식 wrote:


Non si ricevono spesso messaggi di posta elettronica da 
dydtlr5...@gm.gist.ac.kr. Informazioni sul perché è importante 
<https://aka.ms/LearnAboutSenderIdentification>



Hello all~

I'm trying to draw the "Phonon dispersion" of KTaO3 using Phonopy via 
Quantum Espresso 7.2.


I followed the specfic process as presented 
here(_https://phonopy.github.io/phonopy/qe.html 
<https://phonopy.github.io/phonopy/qe.html>_).


I made the supercell 2x2x2.

But in creating "FORCE_SETS", the following error occurred.:

-

_

_ __ | |__ ___ _ __ ___ _ __ _ _

| '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | |

| |_) | | | | (_) | | | | (_) || |_) | |_| |

| .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, |

|_| |_| |___/

2.16.3

Python version 3.9.13

Spglib version 2.0.2

Calculator interface: qe

Displacements were read from "phonopy_disp.yaml".

1.

*

* Parsing "scf-001.out" failed. *

*

2.

*

* Parsing "scf-002.out" failed. *

*

3.

*

* Parsing "scf-003.out" failed. *

*

FORCE_SETS could not be created.

---

Question) What is a problem??

I didnt' find out the reason.

Would you help me?

Thank you.

Sincerely

P.S I attach all the input file("scf*.in", "header.in", "supercell*.in") 
& output one( "phonopy_disp.yaml", "scf*.out").


Yongsik Lym

Gwangju Institute Science & Technology.


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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] pw.x - choosing starting_magnetization value for specific expected total magnetization

[Paolo Giannozzi]

Actually this is going to change in the next release:
- if -1 < starting_magnetization < 1, it works as described below
- if |starting_magnetization| >= 1, it is the starting magnetization in 
Bohr magnetons


Paolo

On 22/02/2024 16:47, Guido Fratesi wrote:


Dear Abdul,

the starting magnetization is here defined as (N_UP-N_DW)/(N_UP+N_DW) so
a value of 1 means fully polarized, N_UP=N and N_DW=0.

Eg if you want 3muB for an atom having 8 electrons you need to put a
value of 3/8.

To obtain the various minima you may have to sample various initial
configurations. It's not at all guaranteed that the calculation will
keep within the basin that you want, and you may need to reduce the
mixing beta, or possibly to constraint the magnetization during the SCF
cycle, and possibly run a following calculation restarting with that
density but without the constraint.

Are you using DFT+U? If not, adding a very small U (1e-5) and setting
verbosity=high will not change the solution but allow you to track the
occupation of the atomic orbitals in detail during the SCF loop.

HTH,
Guido


--
Guido Fratesi

Associate Professor
Physics Department "Aldo Pontremoli"
University of Milan
Via Celoria 16, 20133 Milan, Italy

Phone: +39 02 503 17348
email: guido.frat...@fisica.unimi.it
web:   https://sites.google.com/site/guidofratesi/

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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Nonexistent atom Error in routine read card

[Paolo Giannozzi]

On 2/19/24 11:53, Parvathy Parameswaran wrote:


Error in routine read_cards (1):

      species    C in ATOMIC_POSITIONS is nonexistent


I presume this is a simple syntax issue


the syntax of your file is correct. The error message might be due to 
the presence of CR-LF or of other non-standard characters (tabulators, 
spurious control-something) in the input file


Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Different results for charged cluster in PHonon 5.1 and 7.2

[Paolo Giannozzi]

On 15/02/2024 09:56, RABONE Jeremy wrote:

It is no great problem since these calculations are fine using finite 
differences, but I was just curious as to what has happened and whether 
it was intentional (i.e. should calculations that were done using the 
old version be considered more approximate).
well, no, the calculations done with the old version were fine. Those 
done with more recent versions (v.6.2 and later) were not: see 
https://gitlab.com/QEF/q-e/-/merge_requests/2281 for explanations. Thank 
you for reporting this


Paolo
--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Fail to generate my pseudopotential

[Paolo Giannozzi]

It is a problem of some old versions of gfortran.

Paolo

On 17/02/2024 03:05, wangzongyi via users wrote:

Dear all

I am trying to generate my pseudopotential under the guide of QE's website

*https://dalcorso.github.io/pslibrary/pslibrary_help.html.*

  I first print   '*./configure*' under the directory of

*/public3/home/scg9084/wzy/qe-6.6*

  after the program is finished, I entered    '*make dir*'  ,however, 
the program shows


Error: Assumed-shape array 'zmat' at (1) cannot be an argument to the 
procedure 'c_loc' because it is not C interoperable


xmltools.f90:797.18:

        cp = c_loc(zvec)

                   1

Consequently, Iwrite the path of the main QE directory in the file 
*QE_path*, after that ,I enter pbe file and print


*. ../make_ps*

but after a few moments, I gained an empty pseudopotential file

What happened?Could you please help me?

Thank you very much

Your since

Zongyi Wang

.

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--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] [EXTERNAL] Re: Error in routine init_us_2 (1): internal error: dimension of interpolation table

[Paolo Giannozzi]

On 2/14/24 18:22, Karkee, Rijan wrote:


Hi Paolo,

I am using the latest version of QE (7.3).


you are right, the latest released version (7.3) has the same problem. 
The current development and soon-to-be-released stable version should work


Paolo


-Rijan

*From:* Paolo Giannozzi 
*Sent:* Wednesday, February 14, 2024 9:39 AM
*To:* Quantum ESPRESSO users Forum 
*Cc:* Karkee, Rijan 
*Subject:* [EXTERNAL] Re: [QE-users] Error in routine init_us_2 (1): 
internal error: dimension of interpolation table

The calculation of a numerical derivative requires to compute some
quantities at k+dk and k-dk. It might happen in some unfortunate cases
that q_1=|k+dk+G| or q_2=|k-dk+G| exceed the maximum value set in the
interpolation tables for \beta(q) (nonlocal projectors).

I think that in the latest version of the code out-of-bounds values are
skipped, so there is no crash (but a tiny error is introduced). I cannot
guarantee it, though. Alternatively, one has to locate where the tables
are allocated and increase their size a bit

Paolo

On 2/12/24 23:30, Karkee, Rijan via users wrote:

Hi QE community,

While running the ph.x calculation for Bi2Te3, I ran into this error

   
%%
       Error in routine init_us_2 (1):
       internal error: dimension of interpolation table
   
%%

It completes the Electri Field Calculations, shows dielectric constant, 
also calculates Effective charges (d Force / dE) in cartesian axis with 
asr applied:

        atom      1Bi    Mean Z*:        7.08468
        E*x (        8.24990       -0.0       -0.0 )
        E*y (        0.0        8.24990       -0.0 )
        E*z (       -0.0       -0.0        4.75424 )
             atom      2Bi    Mean Z*:        7.08468
        E*x (        8.24990       -0.0        0.0 )
        E*y (        0.0        8.24990       -0.0 )
        E*z (       -0.0       -0.0        4.75424 )
             atom      3Bi    Mean Z*:        7.08489
        E*x (        8.25032       -0.0       -0.0 )
        E*y (        0.0        8.25032       -0.0 )
        E*z (       -0.0       -0.0        4.75403 )
.
And then stops after
   Calling punch_plot_e
       Writing on file  drho

       Computing Pc [DH,Drho] |psi>

       Derivative coefficient:  0.001000    Threshold: 1.00E-12


   
%%
       Error in routine init_us_2 (1):
       internal error: dimension of interpolation table
   
%%

My 
https://urldefense.com/v3/__http://scf.in__;!!Bt8fGhp8LhKGRg!B8qGM3eY7I6ls08ee3azXoXsWGBhGUcnLyT08T_ihlrTcFSuroOiAJoTPFKH9MHT0OAalXdN2fafPyByMzkVmCYBrlQ$
 
<https://urldefense.com/v3/__http://scf.in__;!!Bt8fGhp8LhKGRg!B8qGM3eY7I6ls08ee3azXoXsWGBhGUcnLyT08T_ihlrTcFSuroOiAJoTPFKH9MHT0OAalXdN2fafPyByMzkVmCYBrlQ$>
  ran with no error  (shown below the input)

      calculation = 'scf'
      pseudo_dir  = '/lustre/scratch4/turquoise/rkarkee/pseudo'
          outdir       = './'
          prefix = 'BiTe'
          tprnfor = .true.
      tstress = .true.
/


      ecutwfc     =  90,
      ibrav       = 0,
      nat         = 15,
      ntyp        = 2,
!  occupations='tetrahedra'
!       noncolin = .true.
!    lspinorb = .true.

/


      conv_thr         =  1.0e-10
      electron_maxstep = 200
      mixing_beta      =  7.0e-01
      diagonalization  = "david"


/

ion_dynamics='fire'
/

press_conv_thr=0.01
/

K_POINTS {automatic}
8 8 2 1 1 1


ATOMIC_SPECIES
Bi     208.9804  Bi.upf
Te      127.60  Te.upf


CELL_PARAMETERS (angstrom)
     4.354840746   0.0   0.0
    -2.177420373   3.771402716   0.0
    -0.0   0.0  29.863328832

ATOMIC_POSITIONS (crystal)
Bi              -0.00        0.00        0.4002380211
Bi              -0.00        0.00        0.5997619789
Bi               0.666870        0.333430        0.7335713665
Bi               0.666870        0.333430        0.9330952695
Bi               0.333430        0.666870        0.0669047085
Bi               0.333430        0.666870        0.2664286035
Te               0.00       -0.00        0.2088757429
Te              -0.00       -0.00        0.7911242721
Te               0.666870        0.333430        0.5422091044
Te               0.666870        0.333430        0.1244576093
Te               0.333430        0.666870        0.8755423987
Te               0.333430        0.666870        0.4577909256
Te              -0.00        0.00       -0.00
Te        

Re: [QE-users] [Probelm] Error in routine natomwfc_per_atom (1): m_start > m_end

[Paolo Giannozzi]

Your Ti and O pseudopotential files do not contain atomic wavefunctions. 
When using Hubbard U with the "ortho-atomic" option, atomic 
wavefunctions are required, also on atoms without a Hubbard U term, I 
think. With "atomic" option, it should work.


Paolo

On 14/02/2024 07:22, 임용식 wrote:


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Hello all~

I'm now calculating the "vc-relax" of EuTiO3 material using Scalar 
relativistic pseudopotentials. This material is antiferromanetic since 
Eu atoms consist of up & down magnetization uniformly.


Recently, the problem occured while calculating "vc-relax" . The error 
message is as follows:




Error in routine natomwfc_per_atom (1):

m_start > m_end



I don't know how to solve this problem. Although I searched the internet 
to solve this problem, I couldn't find appropriate solution.


Please help me.

Thank you.

P.S     I attach Input file("scf.in") & Output one("stdout.txt").



Yongsik Lym

Gwangju Institute Science & Technology.


*보낸 사람:* 임용식
*보낸 날짜:* 2024년 2월 14일 수요일 오후 3:17
*받는 사람:* users@lists.quantum-espresso.org 


*제목:* [Probelm] Error in routine natomwfc_per_atom (1): m_start > m_end

Hello all~

I'm now calculating the "vc-relax" of EuTiO3 material using Scalar 
relativistic pseudopotentials. This material is antiferromanetic since 
Eu atoms consist of up & down magnetization uniformly.


Recently, the problem occured while calculating "vc-relax" . The error 
message is as follows:




Error in routine natomwfc_per_atom (1):

m_start > m_end



I don't know how to solve this problem. Although I searched the internet 
to solve this problem, I couldn't find appropriate solution.


Please help me.

Thank you.

Yongsik Lym

Gwangju Institute Science & Technology.


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Re: [QE-users] Error compiling QE 7.3

[Paolo Giannozzi]

If you type "git --version" what do you get?

Paolo

On 2/15/24 12:27, Federico Verdicchio wrote:


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Dear All,
I'm pretty new to QE and Unix environment in general.
Wanting to explore QE I downloaded the source code from their site. The 
configuration was successful but when trying to compile the program with 
make I get this error:
/Initialised empty Git repository in 
/home/qe/external/lapack/.git/ usage: git remote add []  
 -f, --fetch fetch the remote branches --tags import all tags and 
associated objects when fetching or do not fetch any tag at all 
(--no-tags) -t, --track  branch(es) to track -m, --master 
 master branch --mirror[=(push|fetch)] set up remote as a mirror 
to push to or fetch from /

/fatal: 'origin' does not appear to be a git repository
//fatal: Could not read from remote repository.
//Please make sure you have the correct access rights and the repository 
exists. /
/fatal: 'FETCH_HEAD' is not a commit and a branch 'recorded_HEAD' cannot 
be created from it

//make[1]: *** [extlibs_makefile:23: liblapack] Error 128
make[1]: Leaving directory '/home/qe/install' make: *** [Makefile:228: 
liblapack] Error 2/
I tried on a windows machine using minGW/msys2, with a VM, and on a 
Linux machine running Ubuntu.

Does anyone know How to solve this? Thank you so much!

With regards,
Federico

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Re: [QE-users] Error in routine init_us_2 (1): internal error: dimension of interpolation table

[Paolo Giannozzi]

The calculation of a numerical derivative requires to compute some 
quantities at k+dk and k-dk. It might happen in some unfortunate cases 
that q_1=|k+dk+G| or q_2=|k-dk+G| exceed the maximum value set in the 
interpolation tables for \beta(q) (nonlocal projectors).


I think that in the latest version of the code out-of-bounds values are 
skipped, so there is no crash (but a tiny error is introduced). I cannot 
guarantee it, though. Alternatively, one has to locate where the tables 
are allocated and increase their size a bit


Paolo

On 2/12/24 23:30, Karkee, Rijan via users wrote:

Hi QE community,

While running the ph.x calculation for Bi2Te3, I ran into this error

  %%
      Error in routine init_us_2 (1):
      internal error: dimension of interpolation table
  %%

It completes the Electri Field Calculations, shows dielectric constant, 
also calculates Effective charges (d Force / dE) in cartesian axis with 
asr applied:

       atom      1Bi    Mean Z*:        7.08468
       E*x (        8.24990       -0.0       -0.0 )
       E*y (        0.0        8.24990       -0.0 )
       E*z (       -0.0       -0.0        4.75424 )
            atom      2Bi    Mean Z*:        7.08468
       E*x (        8.24990       -0.0        0.0 )
       E*y (        0.0        8.24990       -0.0 )
       E*z (       -0.0       -0.0        4.75424 )
            atom      3Bi    Mean Z*:        7.08489
       E*x (        8.25032       -0.0       -0.0 )
       E*y (        0.0        8.25032       -0.0 )
       E*z (       -0.0       -0.0        4.75403 )
.
And then stops after
  Calling punch_plot_e
      Writing on file  drho

      Computing Pc [DH,Drho] |psi>

      Derivative coefficient:  0.001000    Threshold: 1.00E-12


  %%
      Error in routine init_us_2 (1):
      internal error: dimension of interpolation table
  %%

My scf.in ran with no error  (shown below the input)

     calculation = 'scf'
     pseudo_dir  = '/lustre/scratch4/turquoise/rkarkee/pseudo'
         outdir       = './'
         prefix = 'BiTe'
         tprnfor = .true.
     tstress = .true.
/


     ecutwfc     =  90,
     ibrav       = 0,
     nat         = 15,
     ntyp        = 2,
!  occupations='tetrahedra'
!       noncolin = .true.
!    lspinorb = .true.

/


     conv_thr         =  1.0e-10
     electron_maxstep = 200
     mixing_beta      =  7.0e-01
     diagonalization  = "david"


/

ion_dynamics='fire'
/

press_conv_thr=0.01
/

K_POINTS {automatic}
8 8 2 1 1 1


ATOMIC_SPECIES
Bi     208.9804  Bi.upf
Te      127.60  Te.upf


CELL_PARAMETERS (angstrom)
    4.354840746   0.0   0.0
   -2.177420373   3.771402716   0.0
   -0.0   0.0  29.863328832

ATOMIC_POSITIONS (crystal)
Bi              -0.00        0.00        0.4002380211
Bi              -0.00        0.00        0.5997619789
Bi               0.666870        0.333430        0.7335713665
Bi               0.666870        0.333430        0.9330952695
Bi               0.333430        0.666870        0.0669047085
Bi               0.333430        0.666870        0.2664286035
Te               0.00       -0.00        0.2088757429
Te              -0.00       -0.00        0.7911242721
Te               0.666870        0.333430        0.5422091044
Te               0.666870        0.333430        0.1244576093
Te               0.333430        0.666870        0.8755423987
Te               0.333430        0.666870        0.4577909256
Te              -0.00        0.00       -0.00
Te               0.666870        0.333430        0.42
Te               0.333430        0.666870        0.666958

Then ph.x input is as follow
Strain Raman Calculation

  tr2_ph=1.0d-16,
  prefix='BiTe',
  trans=.true.,
  epsil=.true.
  lraman=.true.
  outdir='./',
  fildyn='HfTe5.dynG',
  alpha_mix=0.4,
  nmix_ph=8
  max_seconds=169200,
/
0 0 0

Thanks

Best
Rijan



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Re: [QE-users] using ESM with boundary condition "bc1" for charged slab

[Paolo Giannozzi]

I inquired with the author of ESM and this is what he told me:
"Since BC1 has no screening medium in the system, we need to keep charge 
neutral in the DFT cell. Otherwise, the total energy is diverging. In 
the earlier versions, the manual included a note for such charge 
neutrality condition, but for added safety, a routine to check this has 
been incorporated into the program.


In an ESM-RISM calculation, even when using BC1, there is no need to 
impose the charge neutrality condition in the DFT cell, as the RISM part 
automatically generates a compensating charge to maintain the charge 
neutrality condition throughout the whole system."


Paolo

On 2/9/24 06:07, Ghosh, Prasenjit wrote:


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Dear all,

I am performing a calculation for a negatively charged slab using
assume_isolated = 'esm'
esm_bc = 'bc1'

Till qe-7.0 the scf calculation proceeds. However, from version 7.1 the 
calculation stops with the following error:

"cannot have charge, when ESM-BC1".

This is the consequence of a check by the "esm_check" subroutine. What I 
fail to understand is that this check is also present in qe-6.8, 
however, there the calculation doesn't stop.

Am I missing something?
Also why is this stopped from version 7.1. Are there any issues in the 
previous versions regarding the implementations of the same? I thought 
that this is an effective way to perform charged slab calculations.


Any help in clarifying this will be highly appreciated.

With regards,
Prasenjit


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Re: [QE-users] Different results for charged cluster in PHonon 5.1 and 7.2

[Paolo Giannozzi]

On 2/14/24 11:14, RABONE Jeremy wrote:

   I have re-run a Phonon calculation for a charged cluster that was 
done using version 5.1 with version 7.2 and the results are completely 
different; there is a large positive shift in the frequencies. Can 
somebody tell me what was done differently in 5.1 for charged cells ?


no, nobody can: v.5.1 is almost 10 years old. All that can be done is to 
investigate whether the results for a specific case are correct for the 
latest version are correct, and if not, why


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

[Paolo Giannozzi]

On 1/29/24 11:26, Chirantan Pramanik wrote:


'Error in routine phq_readin (1): Wrong nmix_ph'

there is no such error anywhere in the phonon code

Paolo
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Re: [QE-users] GPU and CPU jobs

[Paolo Giannozzi]

On 22/01/2024 14:15, 526587466--- via users wrote:

How to run one GPU and another CPU job (QE7.3 version) in one node?  It 
seems that it sometimes cannot work in one node synchronously.


I don't understand what you mean. If you want to run on GPU's (Nvidia 
for now), you have to compile the code with the HPC SDK of NVidia, then 
launch it (with mpirun). Each MPI process will start on a CPU, will bind 
to a GPU and execute on either CPU or GPU according to what the code is 
instructed to do. This is all you can (and should) do.


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

[Paolo Giannozzi]

There is a temporary problem on the web site

Paolo

On 1/18/24 10:42, Piotr Szkudlarek wrote:


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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

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Re: [QE-users] SCF convergence issue after first ionic step

[Paolo Giannozzi]

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Re: [QE-users] Error while performing Phonon calculations

[Paolo Giannozzi]

It worked for me with the attached scf data

P.
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On 12/18/23 16:06, Lawan, Mukhtar wrote:


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Dear Paolo and other QE Users,


I followed your suggestions with regard to the previous emailand 
attempted to rerun the calculations with more symmetric atomic 
positions, but unfortunately, the error persists. Intriguingly, when I 
calculated the phonons at the gamma point, there was no error encountered.


In my pursuit of a solution, I came across a suggestion online 
(https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33029.html <https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33029.html>) to modify the file PW/src/wsweight.f90. Specifically, I tried changing the value of the parameter nx from 2 to 3, and also experimented with increasing eps to 1.d-5. Despite these attempts, the error persists.


I am reaching out to inquire if there are any other suggestions or 
potential solutions you might recommend. I would be very grateful for 
any further insights you could provide.


Thank you once again for your time and support.


Best regards,

Mukhtar


Doctoral Student at the Theory group of Prof. Dr. Angel Rubio,
Max Planck Institute for Structure and Dynamics of Matter,
Luruper Chaussee 149, 22761 Hamburg, Germany

----
*From:* Paolo Giannozzi 
*Sent:* Friday, December 15, 2023 12:54:59 PM
*To:* Quantum ESPRESSO users Forum; Lawan, Mukhtar
*Subject:* Re: [QE-users] Error while performing Phonon calculations
External Email


Not sure what the specific origin of your problem is, but I guess it is
due to the small breaking of symmetry due to initial atomic positions +
variable-cell noise + option "nosym" (that should not be used except in
some special cases). Try to re-run the self-consistency with more
symmetric atomic positions.

Paolo

On 12/14/23 12:18, Lawan, Mukhtar wrote:


Dear Quantum ESPRESSO Community,

I hope this email finds you well. I am writing to seek assistance
regarding an issue I have encountered while performing phonon dispersion
calculations for a photodoped Bulk MoS2 using Quantum ESPRESSO version 7.2.

To provide some context, I have successfully executed vc-relax
calculations and subsequent phonon calculations on a grid point for Bulk
MoS2. However, when attempting to run q2r.x, I encountered the following
error:

"Error in routine init (1):
q not allowed"

Interestingly, when I conducted similar calculations for monolayer MoS2,
I successfully obtained the phonon dispersion without any issues.

Despite attempting to troubleshoot by adjusting grid points, the error
persists. For your reference, I have attached the input files I utilized
for these calculations.

I am reaching out to the community in the hope that someone may have
insights or suggestions on how to resolve this specific issue. Has
anyone else faced a similar challenge with phonon dispersion
calculations for bulk systems in QE 7.2? Your guidance and expertise
would be invaluable.


Best regards,


Mukhtar Lawan


Doctoral Student at the Theory group of Prof. Dr. Angel Rubio,

Max Planck Institute for Structure and Dynamics of Matter,

Luruper Chaussee 149, 22761 Hamburg, Germany

mukhtar.la...@mpsd.mpg.de


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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216



calculation  = 'scf',
prefix   = 'mos2_2h',
outdir   = './tmp',
twochem   = .true.
tstress = .true., tprnfor = .true.
/

ibrav   = 4,
celldm(1)   = 5.93693513,
celldm(3)   = 3.83047050,
nat = 6,
ntyp= 2,
ecutwfc = 80,
occupations = 'smearing',
degauss = 0.005
nelec_cond = 0.01
degauss_cond = 0.02
nbnd_cond = 4
/

conv_thr = 1.0e-10
electron_maxstep = 100,
mixing_mode  = 'plain'
mixing_beta  = 0.1
/
ATOMIC_SPECIES
Mo 95.96   Mo.pz-hgh.UPF 
S  

Re: [QE-users] Error in routine scale_h (1): Not enough space allocated for radial FFT...

[Paolo Giannozzi]

If you keep the c axis and the Bravais lattice fixed, you do not need to 
perform variable-cell structural optimization: just do a few 
calculations with (slightly) different in-plane lattice parameter(s).


In any event, please provide the test that doesn't work: I want to get 
rid of the "not enough space" error, am quite close to it, and may need 
a test


Paolo

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On 12/14/23 16:30, Dr. Pabitra Mandal wrote:


Non si ricevono spesso messaggi di posta elettronica da 
pabitram.so...@wbnsou.ac.in. Informazioni sul perché è importante 
<https://aka.ms/LearnAboutSenderIdentification>



Dear Pietro,
I am sorry. By mistake I said that my material is  two dimensional. 
Rather it has a layered structure. There will be relaxation along 
z-direction also in the thin layer of the atoms. However to have a 
layered structure, c-axis is set to be large and made fixed by

cell_dofree = 'ibrav + c'
What would be the solution in that case? Please help.
With regards,
pabitra



On Thu, Dec 14, 2023 at 8:41 PM Pietro Davide Delugas <mailto:pdelu...@sissa.it>> wrote:



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  namelist
hope this helps
best regards
Pietro

*Fvalues ofrom:* users mailto:users-boun...@lists.quantum-espresso.org>> on behalf of Dr.
Pabitra Mandal mailto:pabitram.so...@wbnsou.ac.in>>
*Sent:* Thursday, December 14, 2023 15:30
*To:* Quantum ESPRESSO users Forum mailto:users@lists.quantum-espresso.org>>
*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 mailto:users-boun...@lists.quantum-espresso.org>> on behalf of Dr.
Pabitra Mandal mailto:pabitram.so...@wbnsou.ac.in>>
*Sent:* Thursday, December 14, 2023 15:30
*To:* Quantum ESPRESSO users Forum mailto:users@lists.quantum-espresso.org>>
*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

[Paolo Giannozzi]

On 12/13/23 01:49, Saiyed Tasnim Md Fahim wrote:


I am getting the following error:


I am getting a different one with your data:

 Error in routine average_pp (1):
 Fully relativistic PPs, need spin-orbit calc. (lspinorb=.true.)

Paolo
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At line 813 of file xmltools.f90

Fortran runtime error: End of file


I have used the following input file:



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'

/



degauss = 1.4699723600d-02

ecutrho = 4.00d+02

ecutwfc = 5.00d+01

ibrav = 0

nat = 30

nosym = .false.

ntyp = 3

occupations = 'smearing'

smearing = 'cold'

/



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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Re: [QE-users] Spatial dependency of the wave functions for the spin-orbit coupling calculation

[Paolo Giannozzi]

Plane-wave coefficients are complex: the real part is followed by 
imaginary part. The first 2*npw coefficients are for the "up" components 
of the spinor; the following 2*npw are for the "down" component


Paolo
--
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*** AVAILABLE POST-DOC POSITION:
*** https://physicslab.uniud.it/persone/paolo-giannozzi/advert

On 12/12/23 11:25, Alireza Shabani via users wrote:

Dear Giovanni,

Thank you for your explanation. Yes, I think for the number of KS 
states, you are right, as the spin-orbit coupled states are twice the 
non-spin-orbit coupled states. But I am going to focus on just one of 
these states and calculate the wave function using the information in 
the .hdf5 file and equation psi = sigma (C_real + i C_imag) * exp(iG.r), 
which I know I must change a little bit because of the two-component 
spinor.


My question is, is it right to say for every single 'Miller Indices' in 
the .hdf5,we have four complex 'evc'? If so, how should we write the 
vector to form the desired wave function? Is it a vector with two 
complex components like this: (c_1 + j c_2   c_3 +j c_4) * 
exp(iG.r)   ,here c_i are the 'evc'.


Unfortunately, I didn’t find the mathematical description for 
constructing the spinor plane wave in QE, so I would appreciate it if 
anybody could introduce a reference for it.


Thank you for your suggestions.

Alireza Shabani

Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark

*From:*Giovanni Cantele 
*Sent:* Monday, December 11, 2023 2:14 PM
*To:* Alireza Shabani ; Quantum ESPRESSO users Forum 

*Subject:* Re: [QE-users] Spatial dependency of the wave functions for 
the spin-orbit coupling calculation


I'm not expert about HDF5 files, however because you are seeking for 
wave function coefficients, the answer might be that, as explained for 
example here


https://www.quantum-espresso.org/Doc/pw_user_guide/node10.html#SECTION00043030
 
<https://www.quantum-espresso.org/Doc/pw_user_guide/node10.html#SECTION00043030>

when spin-orbit is turned on the wave functions are two-component spinors.
This also reflect the fact that, with nelec electrons, the ground-state 
density suffices nelec/2 Kohn-Sham states (using spin degeneracy) in the 
absence of spin-orbit


coupling, whereas including the latter you need to compute (for 
semiconductors) at least nelec states.


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 <mailto:giovanni.cant...@spin.cnr.it>
Phone: +39 081 676910
Skype contact: giocan74

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


Il giorno lun 11 dic 2023 alle ore 13:49 Alireza Shabani via users 
<mailto:users@lists.quantum-espresso.org>> ha scritto:


Dear QE users,

I am going to calculate the spatial dependency of the wave function
from the output HDF5 files from QE (for one specific k-point, such
as Gamma). I know that the number 'evc' should be twice the 'Miller
Indices' because it includes real and imaginary coefficients in the
wave function: psi = sigma (C_real + i C_imag) * exp(iG.r).

Everything looks fine, and I can calculate the wave function in a
normal DFT calculation (I mean without spin-orbit coupling!!). But,
when I use spin-orbit coupling, the number of 'evc' in the final
.hdf5 file becomes four times the 'Miller Indices.' For instance, if
I have 100 'Miller Indices, ' I will have 400 'evc' which is a bit
confusing. Does anybody know how we can interpret it?

Thank you for your suggestions.

Kind regards,

Alireza Shabani

Postdoc researcher,
Denmark Technical University
Copenhagen, Denmark

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Re: [QE-users] help for "ATOMIC_POSITIONS (crystal_sg)"

[Paolo Giannozzi]

You should set "nat" to 3, not 5. If you provide Wyckoff positions, 
"nat" in input should be equal to the number of Wyckoff positions.


Paolo
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*** https://physicslab.uniud.it/persone/paolo-giannozzi/advert


On 12/6/23 12:14, Zeli Xu wrote:

[Non ricevi spesso messaggi di posta elettronica da zeli...@insa-rennes.fr. Per 
informazioni sull'importanza di questo fatto, visita 
https://aka.ms/LearnAboutSenderIdentification.]

Dear QE users and developers,
   I am using the tag of "ATOMIC_POSITIONS (crystal_sg)" in cubic perovskite 
system. But the output is always wrong. So I put out my Input file and output here. Could 
you please give me some information or help?
3
input:
 
 calculation = 'scf'
 prefix = 'cspbbr3'
 outdir = './'
 pseudo_dir = './'
 disk_io = 'none'
/


 ibrav=1
 nat=5
 ntyp=3
 ecutwfc=80
 space_group = 221
 A = 5.95
!noncolin = .true.
!lspinorb = .true.
/


 conv_thr=1e-8
/

ATOMIC_SPECIES
   Cs 132.905 Cs.upf
   Pb 207.200 Pb.upf
   Br  79.904 Br.upf

K_POINTS {automatic}
   2 2 2 1 1 1

ATOMIC_POSITIONS (crystal_sg)
  Cs  1a
  Pb  1b
  Br  3c

output:
  %%
  Error in routine read_cards (4):
  end of file reading atomic positions
  %%

  stopping ...
##

   Thanks in advance!

Best,
Zeli
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Re: [QE-users] [QE-GPU] High GPU oversubscription detected

[Paolo Giannozzi]

On 11/30/23 10:24, Yin-Ying Ting wrote:

Could you please provide guidance on resolving the oversubscription 
issue? 


if your job runs on 4 GPUs while pretending to run on one, there is no 
real issue: just ignore the message. If you instruct your job to run on 
4 GPUs but it doesn't, you should report it to your system administrator.


Paolo






Kind regards,

Yin-Ying Ting


On 29.11.23 15:53, Paolo Giannozzi wrote:

On 11/27/23 11:32, Yin-Ying Ting wrote:

Based on the *environment.f90* file, this message is triggered when 
/nproc > ndev * nnode * 2/. If I understand correctly, I have nproc 
(Number of parallel processe)=4, ndev(Number of GPU Devices per Node) 
=4 and nnode (Number of Nodes)=1. This condition seems to be false (4 
> 8). Despite this, the message still appears. All 4 GPUs were active 
during the run.


funny. Even funnier, the number of GPUs actually used does not seem to 
be written anywhere on output.


Add a line printing nproc, ndev, nnode just before the warning is 
issued, recompile and re-run. One (at least) of those numbers is not 
what you expect. Computers are not among the most reliable machines, 
but they should be able to find out who is larger between 4 and 8


Paolo

--

Forschungszentrum Jülich GmbH
Institute of Energy and Climate Research
Theory and Computation of Energy Materials (IEK-13)
E-mail: y.t...@fz-juelich.de





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Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens




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Re: [QE-users] [QE-GPU] High GPU oversubscription detected

[Paolo Giannozzi]

On 11/27/23 11:32, Yin-Ying Ting wrote:

Based on the *environment.f90* file, this message is triggered when 
/nproc > ndev * nnode * 2/. If I understand correctly, I have nproc 
(Number of parallel processe)=4, ndev(Number of GPU Devices per Node) =4 
and nnode (Number of Nodes)=1. This condition seems to be false (4 > 8). 
Despite this, the message still appears. All 4 GPUs were active during 
the run.


funny. Even funnier, the number of GPUs actually used does not seem to 
be written anywhere on output.


Add a line printing nproc, ndev, nnode just before the warning is 
issued, recompile and re-run. One (at least) of those numbers is not 
what you expect. Computers are not among the most reliable machines, but 
they should be able to find out who is larger between 4 and 8


Paolo
--
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*** AVAILABLE POST-DOC POSITION:
*** https://physicslab.uniud.it/persone/paolo-giannozzi/advert
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Re: [QE-users] Compilation error of quantum espresso 7.2 with nvfortran

[Paolo Giannozzi]

The devxlib library in external/devxlib/ was not compiled. You should 
first of all figure out why


Paolo

On 10/24/23 16:03, Collins Nganou wrote:


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Hello everyone,

I am running into nvfortran compilation error of quantum espresso 7.2.

Here is the error:
NVFORTRAN-F-0004-Unable to open MODULE file device_fbuff_m.mod 
(cdiaghg.f90: 236)

NVFORTRAN/x86-64 Linux 23.9-0: compilation aborted
make[1]: *** [../make.inc:16: cdiaghg.o] Error 2

my configuration was set as:
./configure --with-cuda="/opt/nvidia/hpc_sdk/Linux_x86_64/2023/cuda" 
--with-cuda-runtime=12.2 --with-cuda-cc=75 --enable-openmp 
--with-scalapack=yes --with-cuda-mpi=yes 
--libdir="/opt/nvidia/hpc_sdk/Linux_x86_64/2023/math_libs"


Kind regards

Albert


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--
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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] pw.x does not recognize pseudopotential file

[Paolo Giannozzi]

There is no difference in the way pseudopotentials are read between 
serial and parallel execution. In the latter, one processor reads and 
sends the data to all others. Some mpi versions may have strange ideas 
on what the "current directory" is, but if you use absolute paths, this 
is not an issue.


Paolo

--
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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216

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On 10/16/23 15:49, Luiz Felipe wrote:

Dear Mr. Lu,

Thanks for the help, this solves the serial running problem, although it 
does not solve the parallel executing one.


Atenciosamente
Luiz Felipe Pompermaier

*De:* users  em nome de 
ludwigboltzmann.s...@nycu.edu.tw 

*Enviado:* segunda-feira, 16 de outubro de 2023 10:28
*Para:* Quantum ESPRESSO users Forum 
*Assunto:* Re: [QE-users] pw.x does not recognize pseudopotential file
Dear Mr. Pompermaier:


Try to use absolute path instead of relative path?

Best Regards,

HY Lu

在 2023年10月16日 星期一 下午09:24:15 [GMT+8]， Luiz 
Felipe 寫道：



Dear qe community,

Recently, after much trouble, I managed to install qe 7.2 on Debian 11.7 OS.

I have already run the standard tests on the test-suite and except for a 
few epw modules, all passed.


Now I'm running another test on the pw.x module trying to get some known 
values for Si crystal¹.


The problem I'm facing, both with mpi and without, is that the pw.x 
module cannot find the pseudopotential file, although it is rightly 
indexed in the respective folder.


What can I do to fix this mistake?

I have also annexed the .in and .out files, and a print screen of the 
command terminal and the pseudopotential folder.


¹ The tutorial I am following for Si calculations is the one presented 
by Quantum Nerd on the video https://www.youtube.com/watch?v=v1LcTLSIkZI 
<https://www.youtube.com/watch?v=v1LcTLSIkZI>

<https://www.youtube.com/watch?v=v1LcTLSIkZI>

Project: 3.1 Si crystal constant and density | Quantum Espresso Tutorial 
2019 <https://www.youtube.com/watch?v=v1LcTLSIkZI>
You can find the input file and reference output file in: 
https://github.com/quantumNerd/Quantum-Espresso-Tutorial-2019-Projects

www.youtube.com



Thankfully
Luiz Felipe Pompermaier

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Re: [QE-users] question about upf2plotcore.sh

[Paolo Giannozzi]

I guess you should use the latest version, that contains this fix:
---
Author: Lorenzo Paulatto 
Date:   Wed Mar 17 15:04:19 2021 +0100

upf2plotcore despite its promise did not seem to work properly with 
UPFv2, i.e. it would not print the radius R because the awk search 
 did not match the actual tag in the file "

---
Utility "upfconv.x" in upflib/ of newer QE releases should do the same 
("upfconv.x -e ... ") but I don't know how well tested it is


Paolo

On 11/10/2023 06:15, Ishiyama,Takahisa_石山 貴久 wrote:


You don't often get email from takahisa.ishiy...@jp.yazaki.com. Learn 
why this is important <https://aka.ms/LearnAboutSenderIdentification>



Dear users,

I calculate XSpectra. And I wonder which script is used to obtain 
initial wavefunction by upf2plotcore.sh.


Outpit is different using it in qe-6.7 and qe-7.1, especially the 
numerical value and number of data obtained.


I found the difference between the versions below.

In qe-6.7

// { #E3

    if ( $1 != "/,/<\/PP_R>/ { #E3

    if ( $1 != "" && $1 != "" ) { #E4

I don’t know well shell script, and if the difference is critical.

Which version should be used ? latest one?



--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Job stopped on wfcs are random step

[Paolo Giannozzi]

On 07/10/2023 09:11, Aziz Ogutlu wrote:


mpirun pw.x < scf.in > scf.out

When job comes to on scf.out file "Starting wfcs are random" step, it 
stops with segmentation fault error.


1.) out of memory (unlikely for such a small case)
2.) bad compilation, or mathematical libraries not suitable for your 
hardware


Paolo



scf.in file is like this:


     calculation='vc-relax',
     pseudo_dir = '/home/Research/QE/pseudo',
     outdir='./'
     prefix='fec',
     verbosity= 'high',
     wf_collect=.true.,
     tprnfor = .true.,
     tstress = .true.
/

     ibrav=0,
     nat = 4,
     ntyp = 2,
     ecutwfc = 90,
     ecutrho = 800,
     occupations = 'fixed'
     smearing = 'gauss'
     starting_magnetization(1) = 3.0
     starting_magnetization(2) = 3.0
     !noncolin =.true.
     !lspinorb =.true.
     force_symmorphic=.true.
/

     electron_maxstep=500
     conv_thr=1d-08,
     mixing_beta=0.3d0,
     startingwfc='random'
     diagonalization='cg'
/
  
   ion_dynamics='bfgs'
  /

   cell_dynamics = 'bfgs'
  /

ATOMIC_SPECIES
  Fe 55.850 Fe.upf
  C 12.001 C.upf

ATOMIC_POSITIONS crystal
Fe   0.252150   0.252090   0.499625
Fe   0.747590   0.747910   0.499625
C    0.249040   0.750480   0.4774516038
C    0.750060   0.249030   0.5225483962

CELL_PARAMETERS angstrom
   3.4881110791   0.014957   0.00
  -0.008267   3.4881110144   0.00
   0.00   0.00  28.1175561443

K_POINTS automatic
1 1 1 0 0 0

HUBBARD (ortho-atomic)
U Fe-3d 3.0



--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Problems instaling QE-7.2

[Paolo Giannozzi]

On 06/10/2023 22:13, Luiz Felipe wrote:

I was recently attempting to install qe 7.2. on Debian 11.7, but on 
running the tests I got the message that all tests failed.


When looking for the log files I have encountered that the error was a 
"no such file or directory exists", in those files that had something 
written in it.


What am I doing wrong on the installation?


as a strict minimum, you should figure out WHICH file or directory does 
not exist, then why it doesn't exist. Then it will be easy to find what 
went wrong


Paolo
--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Test + Postdoctoral position

[Paolo Giannozzi]

So it works again. As you may have noticed, both the users and 
developers mailing list did not work for several days, due to a 
misunderstanding with our internet provider. Apologies for the inconvenient.


Paolo

On 06/10/2023 19:01, Paolo Giannozzi wrote:
This is a test of the correct functioning of the mailing list. Please 
ignore (explanations later) unless you are interested to a postdoctoral 
position, in which case, please read here:

    https://physicslab.uniud.it/persone/paolo-giannozzi/advert
Paolo


--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
___
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[QE-users] Test + Postdoctoral position

[Paolo Giannozzi]

This is a test of the correct functioning of the mailing list. Please 
ignore (explanations later) unless you are interested to a postdoctoral 
position, in which case, please read here:

   https://physicslab.uniud.it/persone/paolo-giannozzi/advert
Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
___
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Re: [QE-users] Infrared Intensity - unexpected values

[Paolo Giannozzi]

On 9/19/23 20:37, ivanpck-cetmic.unlp.edu.ar via users wrote:

There is no problem or error message with that calculations, but the 
results for the dynmat.out are strange and I don't know how to solve it. 
I mean, the third column, named IR, gives me values greater than 100 
(below). Could somebody help me?


what is the expected order of magnitude of IR intensities for the 
material you are studying?


Paolo
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*** AVAILABLE POST-DOC POSITION:
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Re: [QE-users] Why I can't compute the optical properties of my supercell?

[Paolo Giannozzi]

On 9/12/23 17:09, NAIMI SALMA wrote:

If you mean "Estimated total dynamical RAM >    1072.11 GB" , 
unfortunately I don't have that. Is it necessary to have that much RAM 
for my calculation to be done?


maybe, or maybe not. You may want to follow the advice on how to reduce 
memory usage, in the user guide. Selecting "disk_io='high'" might work, 
at the expenses of increased disk access, unfortunately


Paolo


Kind regards,
----
*From:* Paolo Giannozzi 
*Sent:* Tuesday, September 12, 2023 4:02 PM
*To:* Quantum ESPRESSO users Forum ; 
NAIMI SALMA 
*Subject:* Re: [QE-users] Why I can't compute the optical properties of 
my supercell?

"Exactly", hard to tell, but I would have a look at the estimated memory
for your run: do you have that much memory available?

Paolo

On 9/12/23 16:25, NAIMI SALMA wrote:

Dear experts,

I'm trying to simulate the optical properties of a supercell, but after 
some time from running the calculation, the simulation stops suddenly.


   I attached my input and output in a zip file. Could you please help me 
figure out what's the problem exactly?


Kind regards,


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


--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Why I can't compute the optical properties of my supercell?

[Paolo Giannozzi]

"Exactly", hard to tell, but I would have a look at the estimated memory 
for your run: do you have that much memory available?


Paolo

On 9/12/23 16:25, NAIMI SALMA wrote:

Dear experts,

I'm trying to simulate the optical properties of a supercell, but after 
some time from running the calculation, the simulation stops suddenly.


  I attached my input and output in a zip file. Could you please help me 
figure out what's the problem exactly?


Kind regards,


--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
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Re: [QE-users] Intel MKL Error: Parameter 10 was incorrect on entry to ZGEMM

[Paolo Giannozzi]

I cannot reproduce your problem with different pseudopotentials (I don't 
have those you used)


Paolo

On 9/11/23 09:57, Aziz Ogutlu wrote:

Hi Paolo,

I attached scf.out file.

The error is important for us, because when we use command in slurm 
script, it gives this error:


"forrtl: severe (174): SIGSEGV, segmentation fault occurred"

On 9/9/23 11:41, Paolo Giannozzi wrote:
It is not necessarily a serious problem: most likely it means that the 
output dimension of an array is zero. It may happen under some 
circumstances and if there is not a safeguard in the code you may get 
that message, but it may (or may not) have no consequences. It would 
be useful to see an output where this probel occurs


Paolo

On 08/09/2023 16:23, Aziz Ogutlu wrote:

Dear QE community,

We're using Quantum Espresso 7.1 on HPC system. When we run pw.x like 
this:


...

mpirun pw.x < scf.in > scf.out

...

On scf.out file there is error messages like this:

...

Intel MKL ERROR: Parameter 10 was incorrect on entry to ZGEMM .

...

scf.in file is like this:

...


 calculation='vc-relax',
 pseudo_dir = '/Research/QE/pseudo',
 outdir='./'
 prefix=fec,
 verbosity= 'high',
 wf_collect=.true.,
 tprnfor = .true.,
 tstress = .true.
/

 ibrav=0,
 nat = 4,
 ntyp = 2,
 ecutwfc = 90,
 ecutrho = 800,
 occupations = fixed
 smearing = gauss
 starting_magnetization(1) = 3.0
 starting_magnetization(2) = 3.0
 !noncolin =.true.
 !lspinorb =.true.
 force_symmorphic=.true.
/

 electron_maxstep=500
 conv_thr=1d-08,
 mixing_beta=0.3d0,
 startingwfc='random'
 diagonalization='cg'
/
  
   ion_dynamics='bfgs'
  /

   cell_dynamics = 'bfgs'
   !cell_dofree='2Dxy'
  /

ATOMIC_SPECIES
  Fe 55.850 Fe.upf
  C 12.001 C.upf

ATOMIC_POSITIONS crystal
Fe   0.252150   0.252090   0.499625
Fe   0.747590   0.747910   0.499625
C    0.249040   0.750480   0.4774516038
C    0.750060   0.249030   0.5225483962

CELL_PARAMETERS angstrom
   3.4881110791   0.014957   0.00
  -0.008267   3.4881110144   0.00
   0.00   0.00  28.1175561443

K_POINTS automatic
16 16 1 0 0 0

HUBBARD (ortho-atomic)
U Fe-3d 3.0

...

What can the error be about?





--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Intel MKL Error: Parameter 10 was incorrect on entry to ZGEMM

[Paolo Giannozzi]

It is not necessarily a serious problem: most likely it means that the 
output dimension of an array is zero. It may happen under some 
circumstances and if there is not a safeguard in the code you may get 
that message, but it may (or may not) have no consequences. It would be 
useful to see an output where this probel occurs


Paolo

On 08/09/2023 16:23, Aziz Ogutlu wrote:

Dear QE community,

We're using Quantum Espresso 7.1 on HPC system. When we run pw.x like this:

...

mpirun pw.x < scf.in > scf.out

...

On scf.out file there is error messages like this:

...

Intel MKL ERROR: Parameter 10 was incorrect on entry to ZGEMM .

...

scf.in file is like this:

...


     calculation='vc-relax',
     pseudo_dir = '/Research/QE/pseudo',
     outdir='./'
     prefix=fec,
     verbosity= 'high',
     wf_collect=.true.,
     tprnfor = .true.,
     tstress = .true.
/

     ibrav=0,
     nat = 4,
     ntyp = 2,
     ecutwfc = 90,
     ecutrho = 800,
     occupations = fixed
     smearing = gauss
     starting_magnetization(1) = 3.0
     starting_magnetization(2) = 3.0
     !noncolin =.true.
     !lspinorb =.true.
     force_symmorphic=.true.
/

     electron_maxstep=500
     conv_thr=1d-08,
     mixing_beta=0.3d0,
     startingwfc='random'
     diagonalization='cg'
/
  
   ion_dynamics='bfgs'
  /

   cell_dynamics = 'bfgs'
   !cell_dofree='2Dxy'
  /

ATOMIC_SPECIES
  Fe 55.850 Fe.upf
  C 12.001 C.upf

ATOMIC_POSITIONS crystal
Fe   0.252150   0.252090   0.499625
Fe   0.747590   0.747910   0.499625
C    0.249040   0.750480   0.4774516038
C    0.750060   0.249030   0.5225483962

CELL_PARAMETERS angstrom
   3.4881110791   0.014957   0.00
  -0.008267   3.4881110144   0.00
   0.00   0.00  28.1175561443

K_POINTS automatic
16 16 1 0 0 0

HUBBARD (ortho-atomic)
U Fe-3d 3.0

...

What can the error be about?



--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] question about last steps of vc-relax

[Paolo Giannozzi]

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


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

May I ask - what does it indicate


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



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


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

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


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

For me it is conv_thr =   6.40d-06


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

Paolo


Thank you!
best wishes,
             Konstantin

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

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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] [SPAM] QE7bug

[Paolo Giannozzi]

Actually the "bug" (sort of) was in the 6.7 version, not in the most 
recent ones. The code fails to converge (you set a very small threshold 
for pressure) and stops after resetting the history twice (history is 
reset when the optimization procedure runs into trouble). In v.6.7, it 
stops claiming convergence (not true); in later versions, the code stops 
with no convergence (technically true)


Paolo

On 04/09/2023 02:39, 526587466--- via users wrote:

Dear Developers,

Recently, I did a test about the geometry relaxtion of graphene by 
different QE version (i.e., 6.7, 7.1 and 7.2 version).  Only the 6.7 
version gives the convergened result, while not for the 7.1 and 7.2.  
Please see the attachment.


Is there a bug or other things in the QE 7 version?

Thanks

Roc

Henan Normal University, China


--
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Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Missing empty state in SCF calculation

[Paolo Giannozzi]

On 01/09/2023 18:17, Lorenzo Sponza wrote:


Dear Paolo, thanks for the answer.
I made a check running the same two calculations using the CG
diagonalization scheme instead of Davidson. The issue persists. May I
send you the input files ?


not a good idea, because I don't think it is a bug and don't have a 
solution at hand. You may open an issue on gitlab, though.


Paolo


Best


Le 2023-09-01 16:49, Paolo Giannozzi a écrit :

Iterative diagonalization may occasionally miss one or a few states if
the starting manifold does not contain enough components of the
missing states. As long as you do not miss any states in the occupied
manifold, not a big deal for the ground-state calculation (but not for
the band gap, of course)

Paolo

On 9/1/23 16:41, Lorenzo Sponza wrote:


You don't often get email from lorenzo.spo...@onera.fr. Learn why this
is important <https://aka.ms/LearnAboutSenderIdentification>


Dear all,

I encounter an issue I did not expect and I would like to know why it
happens and how I am suppose to handle it. I'm running an SCF
calculation of a gapped system (occupations = 'fixed'). If I include a
large number of empty bands, these are the energies in Gamma:

-4.8200-4.3169-0.9586-0.5478-0.5196-0.4977-0.0537 0.0095 with
occupations 1. 1. 0. 0. 0. 0. 0. 0.

Instead, if I include only one empty band the result is

-4.8200-4.3169-0.5477 with occupations 1. 1. 0.

It's like in if the latter case I was missing the state at -0.9586 eV.
How it happens ?

I'm rising this issue because I'm checking the gapwidth of a series of
similar systems. I actually thought that it was safe to run simple SCF
calculations with 1 empty state, but I realise that results are
possibly wrong. Shall I mandatorily rely on NSCF calculations or I'm
making a mistake somewhere ?

Best regards

-- Dr. Lorenzo Sponza
Chargé de Recherche au CNRS
Laboratoire d'étude de microstructures (LEM), CNRS-ONERA
29 Avenue de la division Leclerc, 92322 Châtillon
Tel: +33146734464

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--
Dr. Lorenzo Sponza
Chargé de Recherche au CNRS
Laboratoire d'étude de microstructures (LEM), CNRS-ONERA
29 Avenue de la division Leclerc, 92322 Châtillon
Tel: +33146734464
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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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Re: [QE-users] Missing empty state in SCF calculation

[Paolo Giannozzi]

Iterative diagonalization may occasionally miss one or a few states if 
the starting manifold does not contain enough components of the missing 
states. As long as you do not miss any states in the occupied manifold, 
not a big deal for the ground-state calculation (but not for the band 
gap, of course)


Paolo

On 9/1/23 16:41, Lorenzo Sponza wrote:


You don't often get email from lorenzo.spo...@onera.fr. Learn why this 
is important <https://aka.ms/LearnAboutSenderIdentification>



Dear all,

I encounter an issue I did not expect and I would like to know why it 
happens and how I am suppose to handle it. I'm running an SCF 
calculation of a gapped system (occupations = 'fixed'). If I include a 
large number of empty bands, these are the energies in Gamma:


-4.8200-4.3169-0.9586-0.5478-0.5196-0.4977-0.0537 0.0095 with 
occupations 1. 1. 0. 0. 0. 0. 0. 0.


Instead, if I include only one empty band the result is

-4.8200-4.3169-0.5477 with occupations 1. 1. 0.

It's like in if the latter case I was missing the state at -0.9586 eV. 
How it happens ?


I'm rising this issue because I'm checking the gapwidth of a series of 
similar systems. I actually thought that it was safe to run simple SCF 
calculations with 1 empty state, but I realise that results are possibly 
wrong. Shall I mandatorily rely on NSCF calculations or I'm making a 
mistake somewhere ?


Best regards

--
Dr. Lorenzo Sponza
Chargé de Recherche au CNRS
Laboratoire d'étude de microstructures (LEM), CNRS-ONERA
29 Avenue de la division Leclerc, 92322 Châtillon
Tel: +33146734464

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] Problem while running QE

[Paolo Giannozzi]

On 29/08/2023 08:49, Piotr Szkudlarek wrote:
After installing some new packages on my machine I started getting such 
error:  > [...]  Segmentation fault      (core dumped) mpiexec -n 24 --bind-to 

core

Am I right in assuming that the new installation could have removed some 
packages?


I don't think so: the executable should yield a different error if a 
library is missing. More likely, some incompatibility with the libraries 
linked in the executable. You may need to recompile, or maybe just to relink


Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] [QE-GPU] Phonon calculation freezing without explanation

[Paolo Giannozzi]

On 30/08/2023 18:36, Owens, Jonathan (GE Vernova, US) wrote:

In the meantime, I tried the CPU-only version and I still have the same 
issue – it just sits at the same point. I was able to run a simple 
example for silicon on the GPU version without issue. Is it just a speed 
thing?


It might be. A 192-atom phonon calculation takes a lot of time for sure. 
The initialization, especially using Ultrasoft pseudopotentials, takes a 
lot of time and of memory. Your cutoff is quite high.


Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] disk space consumption

[Paolo Giannozzi]

The amount of disk you need varies a lot depending upon what you want to 
do with QE. If you just want to optimize a structure, you may do it 
using almost no disk. To compute the band structure, you need to save 
the self-consistent charge density and you may need to save the 
Kohn-Sham orbitals as well. Same to restart from an incomplete calculation.
The size of files can be estimated from the memory taken by respective 
variables, printed at the end of the initial summary


Paolo

On 30/08/2023 08:35, Konstantin Glazyrin wrote:


Dear All,
I am new with QE, trying out our HPC facility, I apologize in advance 
for any double posting.


Our HPC facility has some restrictions for the disk space. I am trying 
to relax an experimentally solved structure in "scf" mode first. The 
procedure of testing/optimizing for ecut takes ~20 GB for 2 points from 
my 30 GB quota. What are the typical values I should consider for the 
disk space consumption when working with QE? What could be a typical 
quota I should consider as comfortable when working with QE?


Thank you!
best wishes,
              Konstantin

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

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

[Paolo Giannozzi]

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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Random seed for MD calculations

[Paolo Giannozzi]

Thank you for noticing again a problem. It will be fixed in next release:
  https://gitlab.com/QEF/q-e/-/merge_requests/2137
Paolo

On 8/14/23 19:24, Han Hsu (徐翰) wrote:


You don't often get email from han...@ncu.edu.tw. Learn why this is 
important 



Dear Professor Giannozzi, QE developers, and QE users:

Previously, I reported that while the patch file provided by Prof. 
Giannozzi works (namely, not all restart MD calculations got the same 
sequence of the random numbers), a particular sequence of random numbers 
is generated much more frequently than the others: Nearly half of my 
restart calculations got that sequence of random numbers. Now I think I 
have found out the reason why. By modifying Modules/random_numbers.f90, 
in particular, its subroutine "set_random_seed" (lines 74–87), this 
problem can be resolved, as described below.


In the subroutine "set_random_seed" , the parameter "iseed" is generated 
based on the system time (lines 81–84), as shown below. By calling 
"date_and_time", the system time is extracted in terms of eight numbers 
(year, month, ..., milliseonds). Four of these numbers are adopted to 
generate "iseed", including the time difference with respect to UTC (in 
minutes) [itime(4)], and minutes, seconds, and milliseconds 
[itime(6–8)]. Among them, I find the inclusion of itime(4) 
incomprehensible, as this term is a constant based on the location of 
the computer. Remarkably, in the UK, itime(4)= 0, meaning this term has 
ZERO effects on "iseed", so why should it be included anyway? By 
contrast, in my country Taiwan (GMT+8), itime(4)= 480, which results in 
a much larger "iseed" than in the UK, by up to hundreds of times...


CALL date_and_time ( values = itime )
! itime contains: year, month, day, time difference in minutes, hours,
!                 minutes, seconds and milliseconds.
iseed = ( itime(8) + itime(6) ) * ( itime(7) + itime(4) )
irand = randy ( iseed )

Given the above analysis, I modified this subroutine by replacing 
itime(4) with itime(5) (namely, hours), making "iseed" fully 
time-dependent. With this modification, all my test calculations 
(from_scratch and all the restart rounds) got different sequences of 
random numbers. If this modification is correct, perhaps it can be 
included in the next release of Quantum Espresso (7.3)?


Thank you for your suggestions and advice.

Best regards,

Han Hsu

On Sat, Aug 12, 2023 at 1:25 AM Han Hsu (徐翰) > wrote:


Dear Professor Giannozzi

Thank you very much for the patch file. It works!! Now, the random
numbers generated in all rounds of calculations (including
from_scratch and all the restart calculations) are not always
repetitive.

After more tests, however, I noticed that some "random numbers" are
generated much much more frequently than the others. Not
surprisingly, this occurs in both 'andersen' and 'svr' thermostats.
What surprises me is that this occurs on different machines at
different institutes as well. I therefore believe this should be
reported, as further described below.

Again, all the test runs were performed using a 8-atom cell of fcc
Si, with dt = 20, tempw = 600. Each run lasts for 12000 steps,
divided into a from_scratch (steps 1–1000) and 11 restart
calculations (steps 1001–2000, 2001–3000, ..., 11001–12000). Both
'andersen' and 'svr' are tested (nraise = 100). A few representative
results obtained on two different machines are shown below (JobID on
these two machines are very different). In order to print out the
random numbers, additional WRITE statements are added to the patched
dynamics_module.f90 file.


(1) svr (random numbers R1, R2, ..., R_Nf are generated in each step)

In run_4323, same sequence of random numbers were generated in
rounds 2, 4, 6, 8, 10, and 12. In run_6632321 (on a different
machine), same sequence of random numbers were generated in rounds
3, 5, 6, 7, 8, and 12. Furthermore, all these 12 rounds on two
different machines got the same sequence of random numbers...

===
run_4323
===
In pwscf.md.1.out, ...
      Entering Dynamics:    iteration =     1
      rr**2 = R1**2 =  0.5153
      sum_of_gaussians2 = R2**2+...+R_Nf**2 =     26.0457
      Entering Dynamics:    iteration =     2
      rr**2 = R1**2 =  0.0411
      sum_of_gaussians2 = R2**2+...+R_Nf**2 =     14.9090
      Entering Dynamics:    iteration =     3
      rr**2 = R1**2 =  0.2940
      sum_of_gaussians2 = R2**2+...+R_Nf**2 =     20.9707
      Entering Dynamics:    iteration =     4
      rr**2 = R1**2 =  1.0311
      sum_of_gaussians2 = R2**2+...+R_Nf**2 =     23.6863
      Entering Dynamics:    iteration =     5
      rr**2 = R1**2 =  0.0971
      sum_of_gaussians2 = R2**2+...+R_Nf**2 =      8.4677
      Entering 

Re: [QE-users] Random seed for MD calculations

[Paolo Giannozzi]

e same pattern persists: In the restart 
calculations, at the same respective time steps (e.g. steps 1001, 2001, 
3001, ...), the same atoms are "randomly" chosen to interact with the 
heat bath.


Finally, my understanding is that in Quantum Espresso, generation and 
seed of random numbers are controlled by Modules/random_numbers.f90 and 
a subroutine set_random_seed(). To properly set the random seed in 
restart calculations, perhaps the subroutine set_random_seed() should be 
called somewhere? (Probably not in dynamics_module.f90, as we do not 
want to reseed the random number in every time step...)


Any suggestions and advice are appreciated. Thank you very much for the 
help!!



Best regards,


Han Hsu
Department of Physics
National Central University (Taiwan)

--
===
  Han Hsu (徐翰)
  Associate Professor
  Department of Physics
  National Central University
  Taoyuan 32001, Taiwan
  Email: han...@ncu.edu.tw <mailto:han...@ncu.edu.tw>
  Web: sites.google.com/site/hanhsuphys 
<https://sites.google.com/site/hanhsuphys/>

  Tel: +886-3-422-7151 ext 65303
  Fax: +886-3-425-1175
===

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222diff --git a/PW/src/dynamics_module.f90 b/PW/src/dynamics_module.f90
index 37416c268..5ea6f9564 100644
--- a/PW/src/dynamics_module.f90
+++ b/PW/src/dynamics_module.f90
@@ -237,7 +237,7 @@ CONTAINS
 is_restart = .FALSE.
  ENDIF
   ENDIF
-
+  !
   IF (.NOT.is_restart) THEN
  !
  CLOSE( UNIT = 4, STATUS = 'DELETE' )
@@ -711,17 +711,13 @@ CONTAINS
  USE symm_base,  ONLY : invsym, nsym, irt
  USE cell_base,  ONLY : alat
  USE ions_base,  ONLY : nat, if_pos
- USE random_numbers, ONLY : gauss_dist, set_random_seed
+ USE random_numbers, ONLY : gauss_dist
  !
  IMPLICIT NONE
  !
  INTEGER  :: na, nb
  REAL(DP) :: total_mass, kt, sigma, ek, ml(3), system_temp
  !
- ! ... next command prevents different MD runs to start
- ! ... with exactly the same "random" velocities
- !
- CALL set_random_seed( )
  kt = temperature / ry_to_kelvin
  !
  ! ... starting velocities have a Maxwell-Boltzmann distribution
diff --git a/PW/src/setup.f90 b/PW/src/setup.f90
index fcbc9a0f7..22f4efb57 100644
--- a/PW/src/setup.f90
+++ b/PW/src/setup.f90
@@ -97,6 +97,8 @@ SUBROUTINE setup()
   USE additional_kpoints, ONLY : add_additional_kpoints
   USE control_flags,  ONLY : sic
   USE sic_mod,ONLY : init_sic, occ_f2fn, sic_energy
+  USE random_numbers, ONLY : set_random_seed
+  USE dynamics_module,ONLY : control_temp
   !
   IMPLICIT NONE
   !
@@ -703,7 +705,10 @@ SUBROUTINE setup()
  IF (sic_energy) CALL occ_f2fn()
   END IF
   !
-  RETURN
+  ! ... next command prevents different MD runs to start
+  ! ... with exactly the same "random" velocities
+  !
+  IF (lmd.AND.control_temp) CALL set_random_seed( )
   !
 END SUBROUTINE setup
 !
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Re: [QE-users] Error in piezoelectric coefficients calculation (Berry phase)

[Paolo Giannozzi]

On 04/08/2023 16:13, Zimmi Singh wrote:

1) In the nscf calculations, I added the 'nbnd' tag in the input file 
(nscf1.in). However, when examining the output file 
(nscf1.out), the polarization value was displayed as NaN


It happens only if you use many processors and many empty bands. The 
reason is quite stupid: a matrix that should be 1 on the diagonal for 
empty bands is instead equal to the number of processors. This does not 
affect the final result but may produce floating-point overflow when 
computing the determinant. It will be fixed in the next version. For the 
time being, use less empty bands (they are useless anyway for Berry's 
phase calculation)


Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] Error in piezoelectric coefficients calculation (Berry phase)

[Paolo Giannozzi]

On 04/08/2023 16:17, ANAND JHA wrote:


That's because nbnd is only used for calculation type BANDS


not really: the number of bands can be specified for any kind of 
calculation. It is typically, but not always, used for "bands" calculations.


The NaN (Not a Number) sgnals a floating-point error typically, overflow 
or division by zero. It appears only for nbnd > 54, though: for smaller 
values of nbnd it works for me. Not sure why


Paolo

On Fri, 4 Aug 2023 at 19:43, Zimmi Singh  
wrote:


Dear Users,

I am attempting to calculate the piezoelectric coefficients of 2D
MoS2 using the Berry Phase method on a strained structure (0.5% in
the armchair direction).

I faced two issues during the process.

1) In the nscf calculations, I added the 'nbnd' tag in the input
file (nscf1.in <http://nscf1.in>). However, when examining the
output file (nscf1.out), the polarization value was displayed as NaN
(see below). I have attached the output file for your reference.

                             VALUES OF POLARIZATION
                              ~~

         The calculation of phases done along the direction of vector 2
         of the reciprocal lattice gives the following contribution to
         the polarization vector (in different units, and being Omega
         the volume of the unit cell):

            P =         NaN  (mod  10.4913000)  (e/Omega).bohr

            P =         NaN  (mod   0.0037363)  e/bohr^2

            P =         NaN  (mod   0.2136113)  C/m^2

         The polarization direction is:  (-0.0 , 1.0 , 0.0 )

However, after removing the 'nbnd' tag in the nscf input file
(nscf.in <http://nscf.in>), I successfully obtained the polarization
values (see below), and also attached the output file (nscf.out)).

                              VALUES OF POLARIZATION
                              ~~

         The calculation of phases done along the direction of vector 2
         of the reciprocal lattice gives the following contribution to
         the polarization vector (in different units, and being Omega
         the volume of the unit cell):

            P =  14.0341794  (mod  10.4913000)  (e/Omega).bohr

            P =   0.0049981  (mod   0.0037363)  e/bohr^2

            P =   0.2857471  (mod   0.2136113)  C/m^2

         The polarization direction is:  (-0.0 , 1.0 , 0.0 )


2) At a strain of 0.5% in the armchair direction, the calculated
polarization vector is P = 0.2857471 C/m². To convert it to C/m, I
multiplied it by the armchair lattice parameter (10.5 angstroms) and
obtained the piezoelectric coefficient e22 = 60006.89 pC/m. However,
the published value for e22 is 362 pC/m (10.1021/acsnano.5b03394).

I have scavenged through the mailing list but found no tutorial on
this topic.

-- 
Best Regards

Zimmi Singh
/Ph.D. Candidate/
/Department of Metallurgical and Materials Engineering
Indian Institute of Technology, Kharagpur
Kharagpur, India/
/Mob No. 9935804727/

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Re: [QE-users] kpoints.x

[Paolo Giannozzi]

<mailto:users@lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
<https://lists.quantum-espresso.org/mailman/listinfo/users>


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Re: [QE-users] How does one calculate dipole moments or access (readable) wave functions from e.g. PW?

[Paolo Giannozzi]

I think code "bands.x" can compute dipole matrix elements.

About direct access to wavefunctions: the default fortran binary format 
is basically unreadable except via the routines of QE. One may 
optionally write hdf5 files that are much easier to read with external 
utilities, though.


Paolo

On 7/25/23 10:40, Brian de Keijzer wrote:

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Hi all,


New QE users here. I’ve used QE so far to compute band structures for crystals. 
I am however very much interested in calculating the dipole matrix elements for 
said crystals. Does QE have a module that allows one to do this? If so, how 
would that work?

Moreover, I have read that it is possible to use the wave functions directly. 
That would allow me to compute the dipole elements. Unfortunately most posts 
that I come across appear to be a bit dated tho. What would be the best way to 
access the wave functions using more recent versions of e.g. Python? I’ve come 
across postqe but that appears to no longer be in development nor does the 
installation work on my Python 3.9 distribution.

Anyhow; I’m looking to learn how to compute k-dependent transition dipole 
moments in QE. It would be awesome if anyone would want to provide an outline 
of how such a thing is to be done using the latest version of QE.


Bests,

Brian de Keijzer
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Re: [QE-users] Missing d orbital in projected band structure of CaC6

[Paolo Giannozzi]

The "3d-1" field in 'config' means - in the rather questionable logic of 
the atomic code - that the 3d orbitals are not bound. In fact the 
pseudization energies for 3d have non-zero values (fourth column below):

3D  3  2  0.00  0.05  1.20  1.70  0.0
3D  3  2  0.00  1.00  1.20  1.70  0.0
The 3d states are thus not saved as atomic states and not usable for 
projection.


Paolo

On 7/25/23 11:12, Giuseppe Mattioli wrote:


Dear Giovanni
I've found this one into the psl-1.0.0 library.

cat > Ca.$fct-spn-rrkjus_psl.1.0.0.in << EOF
  
    title='Ca',
    zed=20.,
    rel=$nrel,
    config='[Ar] 4s2 4p0 3d-1',
    iswitch=3,
    dft='$gfun'
  /
  
    lpaw=.false.,
    pseudotype=3,
    file_pseudopw='Ca.$fct-spn-rrkjus_psl.1.0.0.UPF',
    author='ADC',
    lloc=-1,
    rcloc=1.5,
    which_augfun='PSQ',
    rmatch_augfun_nc=.true.,
    nlcc=.true.,
    new_core_ps=.true.,
    rcore=1.0,
    tm=.true.
  /
6
3S  1  0  2.00  0.00  1.20  1.30  0.0
4S  2  0  2.00  0.00  1.20  1.30  0.0
3P  2  1  6.00  0.00  1.40  1.60  0.0
4P  3  1  0.00  0.00  1.40  1.60  0.0
3D  3  2  0.00  0.05  1.20  1.70  0.0
3D  3  2  0.00  1.00  1.20  1.70  0.0
EOF

Are there two different PPs with the same name out there?
Best
Giuseppe


Quoting Giovanni Cantele :


Dear Bruce,

if I'm not wrong you're using this pseudopotential:
http://pseudopotentials.quantum-espresso.org/upf_files/Ca.pbe-spn-rrkjus_psl.1.0.0.UPF

If you look inside you see that it has been generate with this valence
configuration:
    nl pn  l   occ   Rcut    Rcut US   E pseu
    3S  1  0  2.00  1.200  1.300    -3.461142
    4S  2  0  2.00  1.200  1.300    -0.276804
    3P  2  1  6.00  1.400  1.600    -2.058527
    4P  3  1  0.00  1.400  1.600    -0.103085

As such, when you try to project a band structure of a system containing
this atom, it will only be able to project on 3S, 4S, 3P and 4P states.
You may also check this by looking, inside the UPF file, for the string
PP_GIPAW_ORBITAL
After lines such that
cutoff_radius="0.e0" 
ultrasoft_cutoff_radius="0.e0">
you find the radial part of the corresponding atomic wfc to be used 
for the

projection. Therefore, if an orbital is not included, the code does not
have access to the radial part of the wfc and will not be able to make 
any

projection.

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


Il giorno mar 25 lug 2023 alle ore 09:40 Bruce Wang 


ha scritto:


Dear QE users and developers,

I am currently working on calculating the projected band structure of 
CaC6

using quantum espresso with GGA+UItrasoft pseudopotential (
Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an issue
with obtaining the 3d orbital wavefunctions for Calcium.

I followed the QE PP examples, and I have managed to obtain the 4s 
and 3p

orbitals. The 3d orbital was missing while it should existed.

I would greatly appreciate any guidance on how to retrieve the 3d 
orbital

character of Calcium for my projected band structure calculations.

Thank you for your time and assistance.


Regards,
Bruce
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GIUSEPPE MATTIOLI
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I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: 

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Re: [QE-users] Quantum Espresso installation problem-get Error from "make pw"

[Paolo Giannozzi]

On 7/24/23 17:05, 胡大展 wrote:


My version is gcc 4.8.5


very old, does not work for recent QE versions


I got nothing in "BLAS_LIBS", figure_1.


you got "-lblas", which is what you need

Psolo
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Re: [QE-users] pw.x malloc failed

[Paolo Giannozzi]

The input data you report contain several cases of bad syntax. Please 
provide an input file with correct syntax, the output file and a pointer 
to the pseudopotential files


Paolo

On 7/24/23 13:49, Aziz Ogutlu wrote:


You don't often get email from aziz.ogu...@eduline.com.tr. Learn why 
this is important <https://aka.ms/LearnAboutSenderIdentification>



Hi there all,

We're using Quantum Espresso 7.1 with Intel compiler 2022.3 on HPC system.

When we call pw.x like below, we're getting an error:

/mpirun pw.x -i < scf_step1.in/

...

/Atomic wfc used for Hubbard projectors are NOT orthogonalized//
//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//

//munmap_chunk(): invalid pointer//
//pw.x: malloc.c:4049: _int_malloc: Assertion `(unsigned long) (size) >= 
(unsigned long) (nb)' failed.//

//free(): invalid pointer//
//free(): invalid size//
//munmap_chunk(): invalid pointer//
//forrtl: severe (174): SIGSEGV, segmentation fault occurred/

...

scf_step1.in file is below:

...

///
//    calculation = 'scf'//
//    title = cri3//
//    prefix = cri3//
//    verbosity = high//
//    tprnfor = false//
//    tstress = false//
//    !wf_collect=.true.,//
//    nstep = 100//
//    outdir = '.'//
//    pseudo_dir = '.'//
/

//    ibrav = 0//
//    celldm(1) = 13.2422737624//
//    nat = 8//
//    ntyp = 2//
//    ecutwfc = 40//
//    ecutrho = 480//
//    occupations = smearing//
//    smearing = cold//
//    degauss = 1.0D-1//
//    starting_magnetization(1) = 3.0//
//    starting_magnetization(2) = 3.0//
//    noncolin = true//
//    !lspinorb = true//
//    !force_symmorphic=.true.//
/

//    conv_thr = 1.0D-10//
//    mixing_beta = 1.0D-1//
//    diagonalization = david//
//    electron_maxstep = 100//
/
//CELL_PARAMETERS (alat= 13.24227376)//
//   1.009850542  -0.00028   0.0//
//  -0.504925295   0.874557247   0.0//
//   0.0   0.0   3.053010270//
//
//ATOMIC_SPECIES//
//    Cr   51.9961   Cr.upf//
//    I   126.90447  I.upf//
//
//ATOMIC_POSITIONS (crystal)//
//Cr    0.373212    0.740955    0.537747//
//Cr    0.736698    0.478677    0.537830//
//I 0.6394274459    0.6394360520    0.4263871618//
//I 0.074173    0.3605885769    0.4263860947//
//I 0.3605789168    0.160499    0.4263887410//
//I 0.3605798499    0.3605872226    0.5736275567//
//I 0.6394379899    1.158469    0.5736249512//
//I 1.085003    0.6394365107    0.5736265856//
//
//K_POINTS AUTOMATIC//
//  12 12 1 0 0 0//
//
//HUBBARD atomic//
//U Cr-3d 1.5/

...

--
İyi çalışmalar,
Aziz Öğütlü

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Re: [QE-users] Problem installing unfold.x

[Paolo Giannozzi]

I guess "unfold" was aligned to the latest QE version, that has 
libqefft.a in the FFTXLib/src subdirectory; QE v.7.0 still has 
libqefft.a into the FFTXLib/ subdirectory. If you do not want to compile 
a more recent QE version, try to change the location of the libqefft.a 
library in "unfold" (just grep it)


Paolo

On 21/07/2023 15:10, Paulina Jureczko wrote:



Dear QE developers and users,

I tried to compile the unfold.x with Quantum Espresso v.7.0, but during 
the installation process (I made all of the steps like on the website 
'https://bitbucket.org/bonfus/unfold-x/src/master/'), I faced with the 
following problem:


make[1]: *** No rule to make target 
`/home/paulinaj/qe-7.0/FFTXlib/src/libqefft.a', needed by `unfold.x'.  Stop.

make[1]: Leaving directory `/home/paulinaj/qe-7.0/unfold/src'

I checked in the FFTXlib directory, and there is no 'src' catalogue. 
After several attempts to solve this problem, I do not know how to do it 
and I will appreciate the help.



Bests regards,

Paulina Jureczko

PhD student, Institute of Physics

University of Silesia, Poland


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Re: [QE-users] [QE-GPU] Seeking Step-by-Step Installation Guide for GPU Version of Quantum Espresso (Miguel Urbiztondo)

[Paolo Giannozzi]

Your GPU card seems to be a low-end model. Typically they exhibit 
limited double-precision floating-point performances.


Paolo

On 7/14/23 13:31, Robinson Juma Musembi wrote:
Let me share the steps I followed in installing QE-GPU Quantum Espresso 
7.2 on a desktop with an NVidia GTX 970 and Pop_OS_Nvidia 22.04 Linux 
distro. The following method installs smoothly without error, but pw.x 
there is not much difference in terms of speed, maybe anyone with an 
idea why

step1
start by installing the nvidia hpc_sdk software bundled with cuda
  start by downloading
  $ wget 
https://developer.download.nvidia.com/hpc-sdk/23.3/nvhpc_2023_233_Linux_x86_64_cuda_12.0.tar.gz <https://mailtrack.io/trace/link/22ded0f51fbca542495e3ea216c486b20f1dd97c?url=https%3A%2F%2Fdeveloper.download.nvidia.com%2Fhpc-sdk%2F23.3%2Fnvhpc_2023_233_Linux_x86_64_cuda_12.0.tar.gz=2771463=f13e33fbcab2dbed>

  open the tarball
  $ tar xpzf nvhpc_2023_233_Linux_x86_64_cuda_12.0.tar.gz
  install
  $ sudo nvhpc_2023_233_Linux_x86_64_cuda_12.0/install
  the specify path to local as /usr/local
  export all path given after the installation
  gedit ~/.bashrc
  source ~/.bashrc

step 2
  install quantum espresso-built essentials

step 3
  install cuda aware openmpi
  ./configure --with-cuda=/usr/local/Linux_x86_64/2023/cuda/ 
--prefix=/usr/local/openmpi-4.1.5/

or
if path is as follows
./configure --with-cuda=/usr/local/cuda/ --prefix=/usr/local/openmpi-4.1.5/
then
   sudo make all install
step 4
   sudo apt install git  ==this is required by quantum espresso
step 5
  install quantum espresso
tar -xzvf quantum espresso tar.gz
then
quantum espresso install with cuda libxc and hdf5
./configure --enable-openmp --with-cuda-mpi=yes 
--with-cuda-prefix=/usr/local/2023/cuda --with-cuda-cc=50 
--with-cuda-runtime=12.0
Note that --with-cuda-cc=50 is machine dependent, some machines cc=70, 
or 80 etc


All the following files should have been exported to bashrc

export to bashrc
gedit ~/.bashrc
MANPATH=$MANPATH:/usr/local/Linux_x86_64/23.3/compilers/man; export MANPATH
PATH=/usr/local/Linux_x86_64/23.3/compilers/bin:$PATH; export PATH
export PATH=/usr/local/Linux_x86_64/23.3/comm_libs/mpi/bin:$PATH
export MANPATH=$MANPATH:/usr/local/Linux_x86_64/23.3/comm_libs/mpi/man
export PATH=$PATH:/usr/local/openmpi-4.1.5/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi-4.1.5/lib
export PATH=$PATH:/home/robinsonmusembi/DFT/qe-7.2/bin
source ~/.bashrc

*Robinson J.  Musembi*
Solid State and Materials Research
Department of Physics, University of Nairobi



-
A KEBS 9001:2015 Certified Organization, No. KEBS/QMS/RF:064 Rev. 03


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Re: [QE-users] SIC function in CPV relaxation

[Paolo Giannozzi]

On 7/10/23 14:23, Xichen Hu wrote:


I am trying to use self-interaction correction feature in cp.x package 
to do a relaxation task, but it seems like there are some functions 
which haven’t been implemented yet.


The SIC functionality was implemented many years ago, but nobody 
maintained them, so it has been disabled. You may try to comment out the 
check and see what happens, but it is unlikely to work. It may still 
work in some old versions of QE (how old? no idea, very old presumably)


Paolo
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Re: [QE-users] Why my material do not get optimized with vc-relax using HSE?

[Paolo Giannozzi]

Find the equilibrium lattice parameter "the old way", that is, with a 
E(V) equation of state. There is something wrong with exact-exchange stress


Paolo

On 7/3/23 13:17, NAIMI SALMA wrote:


I tried so many times to do a vc-relax calculation to my material with 
Quantum ESPRESSO . But the material is not converging when using hybrid 
functional like HSE, I do not get the block :


``` Begin final coordinates
  End final coordinates```

How can I solve this problem please?

PS: I attached the input file. I can't attach the output because it's 
too big so I attached also a file that contains the development of 
unit-cell volume, extracted from the output file.



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Phone +39-0432-558216, fax +39-0432-558222
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Re: [QE-users] R: Data Parallelism and GPU Support for Quantum Espresso

[Paolo Giannozzi]

Apparently the intel compiler doesn't like the instruction at line 78 of 
PW/src/manypw.f90 (other compilers don't complain), introduced for the 
reason explained above in the code. As a quick fix, just replace 
STATUS='DELETE' with STATUS='KEEP'.


Paolo


On 02/07/2023 09:41, Prashant Govindarajan via users wrote:
Hi! Thanks a lot for the suggestions. I tried *manypw.x*  just with 2 
input files to see if it works. Basically, my directory consists of 
(drive links of text files provided)


 1. Input 1 -- espresso_0.in
 2. Input 2 -- espresso_1.in
 3. Slurm job script -- script *(1 node, 8 tasks per node, 4 cpus per task, QE 
version 7.0)*

The command I run (on Compute Canada) is the following

srun --cpus-per-task=$SLURM_CPUS_PER_TASK manypw.x -ni 2 -i espresso


When I submit the job, Input 2 starts and it immediately stops with the 
error message as described below, and Input 1 never starts.


--
      Program PWSCF v.7.0 starts on  2Jul2023 at  13:13:48

      This program is part of the open-source Quantum ESPRESSO suite
      for quantum simulation of materials; please cite
          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
          "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
           URL http://www.quantum-espresso.org/ 
<http://www.quantum-espresso.org/>",
      in publications or presentations arising from this work. More 
details at
http://www.quantum-espresso.org/quote 
<http://www.quantum-espresso.org/quote>


      Parallel version (MPI & OpenMP), running on      32 processor cores
      Number of MPI processes:                 8
      Threads/MPI process:                     4

      MPI processes distributed on     1 nodes
      path-images division:  nimage    =       2
      R & G space division:  proc/nbgrp/npool/nimage =       4
      35167 MiB available memory on the printing compute node when the 
environment starts


forrtl: Operation not permitted
forrtl: severe (28): CLOSE error, unit 6, file "Unknown"
Image              PC                Routine            Line        Source
manypw.x           0152002B  for__io_return        Unknown  Unknown
manypw.x           0151221F  for_close             Unknown  Unknown
manypw.x           004C6BAF  Unknown               Unknown  Unknown
manypw.x           00413F67  Unknown               Unknown  Unknown
manypw.x           00413D12  Unknown               Unknown  Unknown
libc-2.30.so 
<http://libc-2.30.so/>       2B46AD812E1B  __libc_start_main     Unknown  Unknown

manypw.x           00413C2A  Unknown               Unknown  Unknown
srun: error: bc11237: task 0: Exited with exit code 28
--

I got the output file for one of the inputs as mentioned before, and it 
almost reaches completion when the above error appears. The output file 
is espresso_1.out 
<https://drive.google.com/file/d/1u43HULHS6VWddnsIhqzhpkTlaCiQIJGD/view?usp=sharing>. My understanding is that it starts for one of the inputs but when it parallely tries to start the other input, it is trying to access something that it does not have permissions. I'm not sure if this is a common error, but I was not able to see a solution for this anywhere. What could be the best way to resolve this? Please let me know if any further information is required from my side.


Actually I have faced similar issues while using just pw.x and having a 
'for loop' over multiple input crystals, so I thought I should find the 
root cause of such errors.


Thanks and Regards
*Prashant Govindarajan*


On Fri, Jun 30, 2023 at 4:34 AM Paolo Giannozzi 
mailto:paolo.gianno...@uniud.it>> wrote:


On 6/30/23 10:27, Pietro Davide Delugas wrote:

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

its usage is described in the header of PW/src/manypw.f90

Paolo
-- 
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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] R: Data Parallelism and GPU Support for Quantum Espresso

[Paolo Giannozzi]

On 6/30/23 10:27, Pietro Davide Delugas wrote:

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


its usage is described in the header of PW/src/manypw.f90

Paolo
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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] maxster increasing for phonon convergence

[Paolo Giannozzi]

On 6/28/23 06:32, Esmaeili via users wrote:

However, It is question for me why changing maxter does not control the 
maximum number of iterations!


it does. Did you recompile?

Paolo


Asghar

On Mon, 05 Tir 1402 11:43 PM, 
Abiodun Odusanya  wrote:


Hi,

Try reducing alpha_mix(1) to 0.1 and increase nmix_ph to 8, that
should solve the problem if your structure is well relaxed.

Abiodun Odusanya

Graduate Assistant of Mechanical Engineering

North Carolina A & T State University

1601 East Market Street

Greensboro, NC 27411

On Mon, Jun 26, 2023, 3:42 PM Esmaeili via users
mailto:users@lists.quantum-espresso.org>> wrote:

​Dear developers,
I'm using qe-7.1. To obtain convergence using pH.x, I increased
maxster in phonon/PH/phcom.f90 from 100 to 250 but the run is
also terminating at 100 iteration without convergence!
I repeated maxster adjusting several times but the number of
iterations doesn't increase.
Would you please let me know how can I increase the number of
iteration in pH.x?

Yours Sincerely,
Asghar
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Univ. Udine, via delle Scienze 208, 33100 Udine Italy, +39-0432-558216
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Re: [QE-users] 2. k-point parallelisation using ESM-RISM: seg fault (Tom Demeyere)

[Paolo Giannozzi]

A bad quote may lead to obscure errors when reading data, or to data 
being written to files with funny names, but it seems to me unlikely 
that it can produce a segmentation fault as shown in the traceback.


Paolo

On 24/06/2023 13:22, Robinson Juma Musembi wrote:


items in quote marks are interpreted as data type string by the 
computer, the error might be triggered by how you have written the prefix


    calculation      = 'relax'
    restart_mode     = 'from_scratch'
    nstep            = 999
    tstress          = .false.
    tprnfor          = .true.
    outdir           = 'pw.dir'
    prefix           = ?pw'
    etot_conv_thr    = 1e-06
    forc_conv_thr    = 0.001
    trism            = .true.
/

*Robinson J.  Musembi*
Solid State and Materials Research
Department of Physics, University of Nairobi



-
A KEBS 9001:2015 Certified Organization, No. KEBS/QMS/RF:064 Rev. 03


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Re: [QE-users] Projwfc.x: Mismatch between the requested and available manifolds

[Paolo Giannozzi]

It is fixed in v.7.2

Paolo

On 6/18/23 04:53, Christoph Wolf wrote:

Hi guys,

I have a slight problem with projwfc and the new Hubbard U formalism.

The scf and nscf finish without any issue using the following Hubbard U 
input:


HUBBARD ortho-atomic
U C-2p 1D-10
U Dy-5d 1
U Dy-6s 1

(C and Dy are there only species, for C I use the PSL PP and for Dy the 
PAW dataset with the latest atompaw which includes proper labels).  
Unfortunately projwfc ends with the following



  Program PROJWFC v.7.1 starts on 18Jun2023 at 11:39:15

      This program is part of the open-source Quantum ESPRESSO suite
      for quantum simulation of materials; please cite
          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
          "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
           URL http://www.quantum-espresso.org 
<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.quantum-espresso.org%2F=05%7C01%7Cpaolo.giannozzi%40uniud.it%7C3c3bad958bdf4830b41d08db6fa7409d%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638226536372193432%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ZRfbx9FToQa8pnmY40Cm4QY77bVAxMKP2N%2FHBW2wm1s%3D=0>",
      in publications or presentations arising from this work. More 
details at
http://www.quantum-espresso.org/quote 
<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.quantum-espresso.org%2Fquote=05%7C01%7Cpaolo.giannozzi%40uniud.it%7C3c3bad958bdf4830b41d08db6fa7409d%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638226536372193432%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=q3vDgobk14byAAMgb%2FguVDJcRIYWhcj2zdSr1UkLSuc%3D=0>


      Parallel version (MPI), running on    40 processors

      MPI processes distributed on     1 nodes
      R & G space division:  proc/nbgrp/npool/nimage =      40
      168388 MiB available memory on the printing compute node when the 
environment starts


      Reading xml data from directory:

      ./tmp/Dy.save/

  %%
      Error in routine offset_atom_wfc (2):
      Mismatch between the requested and available manifolds
  %%

      stopping ...
Is there anything wrong with the way I define the Hubbard input? If I 
don’t apply two manifolds (d and s) it works without any problem.


Thanks in advance for any help! :)

Chris
--
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IBS Center for Quantum Nanoscience
Seoul, South Korea
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Re: [QE-users] Large estimated SCF accuracy for monolayer \alpha-RuCl3

[Paolo Giannozzi]

On 6/21/23 07:29, Lingzhi ZHANG wrote:


I’m conducting GGA+SOC+U+Constrained DFT in QE-7.0.


what do you mean by "constrained DFT" ?


But the estimated SCF accuracy for my system is considerably large in the first 
and the following steps, more enormous than 1 Ry.

I have tried many methods such as modifying the mixing scheme from plain to TF, 
tuning the degauss, and trying different occupation and smearing schemes.
I also tried to start from the GGA+LSDA+U case, which works well and gets 
converged in 700 steps.
But no scheme works for  GGA+SOC+U+Constrained DFT.
And even for just the GGA+SOC+U case, I can't obtain a small SCF accuracy.


Are you sure DFT+U for SOC works with PAW potentials?

Paolo


I’d like to know what I can do for it and get a normal SCF process.

My input is in the following.
This structure was obtained from OpenMX, another DFT package based on the LCAO 
method.


 calculation='scf',
 prefix='mono',
 pseudo_dir='/home/zhang/calculation/rucl3/pseudo',
 restart_mode='from_scratch',
 outdir='./',
 verbosity='high',
/

 ibrav= 0,
 nat= 16, ntyp= 3,
 occupations = 'smearing',
 smearing='mp', degauss=1d-9,
 ecutwfc= 100,
 noncolin=.true.,lspinorb=.true.,
 starting_magnetization(1)= 0.5,
 starting_magnetization(2)= 0.5,
 starting_magnetization(3)= 0.0,
 lda_plus_u = .true.,
 lda_plus_u_kind = 1,
 U_projection_type = 'ortho-atomic',
 Hubbard_U(1)=1.5,
 Hubbard_U(2)=1.5
/

 electron_maxstep = 1600
 conv_thr = 1.0d-8
 mixing_mode = 'TF'
 mixing_beta = 4.0d-2
 mixing_ndim = 20
 startingpot = 'atomic'
 diagonalization = 'david'

/
ATOMIC_SPECIES
Ruu 101.07   Ru.rel-pbe-spn-kjpaw_psl.1.0.0.UPF
Rud 101.07   Ru.rel-pbe-spn-kjpaw_psl.1.0.0.UPF
Cl  35.45Cl.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
 Ruu -2.4165100  0.0119000  2.4251100
 Ruu  0.0032200  0.0119000  0.0053700
 Cl   2.3833500 -0.0499700  0.0334100
 Cl  -2.3884800 -0.0499700  4.8052300
 Cl  -0.0381100  0.0580100  2.3837700
 Cl  -2.3751800 -0.0342100  0.0467100
 Cl  -2.4518700 -2.3681500  2.5014800
 Cl   0.0796000 -2.3681500 -0.0299800
 Rud  0.0105400  2.4538100 -2.4511300
 Rud  2.4302700  2.4538100 -4.8708700
 Cl   4.8104000  2.3919400 -4.8428300
 Cl   0.0385700  2.3919400 -0.0710100
 Cl   2.3889400  2.4999200 -2.4924700
 Cl   0.0518700  2.4077000 -4.8295300
 Cl  -0.0248200  0.0737600 -2.3747600
 Cl   2.5066500  0.0737600 -4.9062200
CELL_PARAMETERS {angstrom}
  4.8541000 4.8838200-9.7524800
 -4.8762300 2.4419100 2.4270500
 10.020330010.018540010.0203300
K_POINTS {automatic}
  6 12 1 0 0 0



The following is part of the output
total energy = -2977.28363823 Ry estimated scf accuracy < 529768.11044287 Ry
total energy = -2977.28363823 Ry estimated scf accuracy < 529768.11044287 Ry
total energy = -3184.06809008 Ry estimated scf accuracy < 814811.34802588 Ry
total energy = -3274.94372181 Ry estimated scf accuracy < 746852.52429958 Ry
total energy = -3307.21972156 Ry estimated scf accuracy < 752237.62011255 Ry
total energy = -3291.26999775 Ry estimated scf accuracy < 757458.22549562 Ry
total energy = -3349.60629608 Ry estimated scf accuracy < 765501.04417510 Ry
total energy = -3337.49045478 Ry estimated scf accuracy < 768896.10678680 Ry
total energy = -3287.13640144 Ry estimated scf accuracy < 762797.72531670 Ry
total energy = -.32846680 Ry estimated scf accuracy < 751861.05720886 Ry
total energy = -3341.65785225 Ry estimated scf accuracy < 754604.69881806 Ry
total energy = -3350.72599779 Ry estimated scf accuracy < 749241.08182438 Ry
total energy = -3366.01560869 Ry estimated scf accuracy < 741018.08470080 Ry



With best regards

Lingzhi Zhang
Department of Applied Physics,
University of Tokyo, Japan
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Re: [QE-users] Error Message while performing SCF.in

[Paolo Giannozzi]

Note that your structure looks funny: Ga-As bond distance 1.35 A

Paolo
On 6/21/23 10:31, Paolo Giannozzi wrote:

On 6/21/23 00:44, Md. Jahid Hasan Sagor wrote:

Can anyone please help to identify why I am getting an error message 
while running the scf.in [] attached here. I couldn't find my mistakes 
to prepare the scf.in 


there isn't any, but there is a missing piece of information here (more 
than one actually): how many MPI processes did you use?


P.


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Re: [QE-users] Error Message while performing SCF.in

[Paolo Giannozzi]

On 6/21/23 00:44, Md. Jahid Hasan Sagor wrote:

Can anyone please help to identify why I am getting an error message 
while running the scf.in [] attached here. I couldn't find my mistakes to prepare the scf.in 


there isn't any, but there is a missing piece of information here (more 
than one actually): how many MPI processes did you use?


P.
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Re: [QE-users] Using SCAN functionals with QE 7.2

[Paolo Giannozzi]

On 6/19/23 16:23, Monteiro Campos de Melo, P.M. (Pedro) via users wrote:

Another question: are there any plans to extend MGGA functionals to 
cases with non-collinear spin?


I don't think it is very difficult, but:
  Meta-GGA = hard to converge
  Non-colinear = hard to converge
  Meta-GGA + Non-colinear = hard^2 to converge

Paolo


Cheers,

Pedro

*From: *Fabrizio Ferrari Ruffino 
*Date: *Monday, 19. June 2023 at 15:53
*To: *Monteiro Campos de Melo, P.M. (Pedro) 
, Quantum ESPRESSO users Forum 


*Subject: *Re: Using SCAN functionals with QE 7.2



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Hello,

are you using dftd3? If so, which dftd3_version (input file)?

Only some selected functionals are allowed with dftd3, scan is usable 
with version 4 only.


Cheers,

Fabrizio



*From:*users  on behalf of 
Monteiro Campos de Melo, P.M. (Pedro) via users 


*Sent:* Monday, June 19, 2023 3:07 PM
*To:* users@lists.quantum-espresso.org 
*Subject:* [QE-users] Using SCAN functionals with QE 7.2

Hello,

I am trying to use the SCAN functional with QE 7.2 and libxc 5.2.3. I 
have found some older threads about what value to assign to input_dft, 
but all the following have failed so far:


“scan”

“r2scan”

“rvv10-scan”

“XC-000i-000i-000i-000i-263L-292L“

“XC-001i-004i-013i-vdw2”

The code stops and prints the error message:

“””

program stopped due to: functional name unknown

STOP must stop!

“””

Could you provide me any guidance on how to overcome this? Is this an 
issue with the libxc version?


Kind regards,

Pedro Melo


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Re: [QE-users] vc-relax with PBE0 or HSE is not converging

[Paolo Giannozzi]

The stress calculation with hybrid functionals is actually implemented, 
but there are still some mysterious problems. See: 
https://gitlab.com/QEF/q-e/-/issues/204


Paolo

On 6/14/23 15:46, Giuseppe Mattioli wrote:


Dear Salma
I don't know how outdated it is, but there is a README in the directory 
of the EXX examples


/path_to_QE_7.2/PW/examples/EXX_example

reporting this:

  WHAT PROPERTIES CAN I COMPUTE ?
   Energy and forces (thanks to Hellmann-Feynman theorem forces do not
   require extra calculations). In principle also stresses but the
   corresponding formulas have not yet been coded. <---!!!
   So structural optimization is OK if the cell shape is kept fixed.

HTH
Giuseppe


Quoting NAIMI SALMA :


Dear all,

I'm doing a vc-relax for my material with hybrid functionals and ONCV 
pseudopotentials.


When the job is done I can't find the optimized final coordinates and 
lattice parameter in the output file , also I noticed that the final 
pressure is positive and not close to zero, as bellow:


 Computing stress (Cartesian axis) and pressure

  total   stress  (Ry/bohr**3)   (kbar) 
P=  106.49
   0.00072391  -0.   0.  106.49   -0.00  
  0.00
  -0.   0.00072391   0.   -0.00  106.49  
  0.00
  -0.  -0.   0.00072391   -0.00   -0.00  
    106.49



 I repeated the calculation so many times by modifying some input  
variables but the same problems always occur for PBE0 and HSE as well.



Before the last lines in the output file I find this:



...

Input lattice vectors:

    -0.50342437 0. 0.50342437

 0. 0.50342437 0.50342437

    -0.50342437 0.50342437 0.

New lattice vectors in INITIAL alat:

    -0.50342437 0. 0.50342437

 0. 0.50342437 0.50342437

    -0.50342437 0.50342437 0.

New lattice vectors in NEW alat (for information only):

    -0.5000 0. 0.5000

 0. 0.5000 0.5000

    -0.5000 0.5000 0.

Discrepancy in bohr = 0.00    0.00    0.00


 The maximum number of steps has been reached.


 End of BFGS Geometry Optimization

 new unit-cell volume =    382.92325 a.u.^3 (    56.74337 Ang^3 )

 density =  5.57333 g/cm^3


CELL_PARAMETERS (alat= 11.44879234)

  -0.503424371   0.0   0.503424371

   0.0   0.503424371   0.503424371

  -0.503424371   0.503424371   0.0


ATOMIC_POSITIONS (crystal)





Where this problem is coming from please and how can I fix it?

I attached my input file








Salma NAIMI
PhD student - Mohamed 5 University-Rabat




GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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E-mail: 

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Re: [QE-users] [D3q-discuss] Error executing d3_q2r.x

[Paolo Giannozzi]

Unrelated: you should not run so many OpenMP threads (48), it is very 
inefficient.


Paolo

On 6/9/23 13:49, Elio Physics wrote:

Dear prof. Paulatto,

Thanks for your quick response. This is weird. I am using the correct  
d3_q2r.x executable. I have taken a screen shot of the error (I have 
attached it to this e-mail).
I am also getting a weird result when I call the d3_asr.x executable.  I 
am getting a lot of "NaN" with no values in the output file (also 
attached a screenshot of the output file).



Thank you for your help

Regards

*From:* Lorenzo Paulatto 
*Sent:* Friday, June 9, 2023 5:09 AM
*To:* d3q-disc...@lists.sourceforge.net 
*Subject:* Re: [D3q-discuss] Error executing d3_q2r.x

Hello Elio,

I copy-pasted your input and it works for me.

The error must be elsewhere (are you sure you're not calli d3_r2q.x 
instead?)


kind regards



On 6/9/23 03:59, Elio Physics wrote:

Dear  all,

I am trying to test the d3q code by reproducing the results for 
Silicon. Everything went fine except when I execute the d3_q2r.x flag 
which applies to the 2^nd order dynamical matrices.  The dynamical 
matrices for the 8 points in the q grid were produced as "matdyn0", 
"matdyn1", "matdyn2",,"matdyn8". My d3_q2r.x input is:



fildyn  =  'matdyn'
flfrc   =  'mat2R'
 /

However the code crashes with the error:

 %%
     Error in routine q2r (1):
     error reading input namelist
 %%

I cannot figure out what is wrong with the input. I tried to rename 
the files as "dyn0", "dyn1", and set fildyn='dyn', but I still get 
the same error. Can anyone spot what the error could be?


Thanks in advance..

Elie Albert Moujaes
Adjunct professor level 4
Federal University of Rondonia
Brazil


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Re: [QE-users] asr in dynmat.x

[Paolo Giannozzi]

to notify them of the error immediately and to then delete the 
email from your inbox and deleted items. Keele University staff and 
students are required to abide by the University's IT Policies when 
sending and receiving email. Keele University email is hosted by a cloud 
provider and may be stored outside of the UK.



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Re: [QE-users] Error when make epw with nvhpc compiler

[Paolo Giannozzi]

On 01/06/2023 18:47, Abiodun Odusanya wrote:


Hi all,

I installed QE v7.2 but epw.x executable was not found in the bin folder 
after make all. What should I do?


for sure, you should do "make epw". "make all" does not compile EOW

Paolo



Regards,

Abiodun Odusanya

Graduate Assistant of Mechanical Engineering

North Carolina A & T State University

1601 East Market Street

Greensboro, NC 27411

On Thu, Jun 1, 2023, 8:29 AM Paolo Giannozzi <mailto:paolo.gianno...@uniud.it>> wrote:


Look into EPW/src/low_lvl.f90: there is a preprocessed line
      INTEGER, EXTERNAL :: getpid
Not sure why it is not correctly preprocessed, but in any event, you
can
just move it out of the #if defined  #endif section

Paolo

On 6/1/23 12:17, Siwakorn Sukharom wrote:
 > I got this error when I want to make epw ( I have done make all
 > successfully)
 >
 > I used nvhpc/22.7 for compilation
 > here is the make.inc
 >
 >
https://drive.google.com/file/d/1OaGkzOJnW11neChoHwLpUanEdYhJNPvt/view?usp=sharing 
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1OaGkzOJnW11neChoHwLpUanEdYhJNPvt%2Fview%3Fusp%3Dsharing=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb64c1fb944834ebf3c2608db62c005bd%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638212349109098630%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=QfP2SybMtecWPItyvGF5NJ7QnM9yijgUxRsdrDx7E74%3D=0>
 
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 >
 > NVFORTRAN-W-0921-Redefinition of symbol _OPENACC
(low_lvl_tmp.f90: -1)
 > NVFORTRAN-S-0038-Symbol, getpid, has not been explicitly declared
 > (low_lvl_tmp.f90)
 >    0 inform,   0 warnings,   1 severes, 0 fatal for system_mem_usage
 > make[2]: *** [../../make.inc:16: low_lvl.o] Error 2
 > make[2]: Leaving directory
 >
'/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu/EPW/src'
 > make[1]: *** [Makefile:7: epw] Error 2
 > make[1]: Leaving directory
 > '/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu/EPW'
 > make: *** [Makefile:129: epw] Error 1
 >
 >
 >
 >

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Re: [QE-users] Error when make epw with nvhpc compiler

[Paolo Giannozzi]

Look into EPW/src/low_lvl.f90: there is a preprocessed line
INTEGER, EXTERNAL :: getpid
Not sure why it is not correctly preprocessed, but in any event, you can 
just move it out of the #if defined  #endif section


Paolo

On 6/1/23 12:17, Siwakorn Sukharom wrote:
I got this error when I want to make epw ( I have done make all 
successfully)


I used nvhpc/22.7 for compilation
here is the make.inc

https://drive.google.com/file/d/1OaGkzOJnW11neChoHwLpUanEdYhJNPvt/view?usp=sharing 
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1OaGkzOJnW11neChoHwLpUanEdYhJNPvt%2Fview%3Fusp%3Dsharing=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cf550edb7f01e4129fe6508db6289775b%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638212114780554217%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=6rLln6Rg5nmkwRUSXPhd4h3QfTBmR296Qj8U16T1%2FAE%3D=0>

NVFORTRAN-W-0921-Redefinition of symbol _OPENACC (low_lvl_tmp.f90: -1)
NVFORTRAN-S-0038-Symbol, getpid, has not been explicitly declared 
(low_lvl_tmp.f90)

   0 inform,   0 warnings,   1 severes, 0 fatal for system_mem_usage
make[2]: *** [../../make.inc:16: low_lvl.o] Error 2
make[2]: Leaving directory 
'/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu/EPW/src'

make[1]: *** [Makefile:7: epw] Error 2
make[1]: Leaving directory 
'/lustrefs/disk/project/thaisc/siwakorn/QE/install/qe-7.2_gpu/EPW'

make: *** [Makefile:129: epw] Error 1





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Re: [QE-users] no geometry information at the end

[Paolo Giannozzi]

ensive has on their
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Re: [QE-users] users Digest, Vol 190, Issue 21

[Paolo Giannozzi]

It's actually possible: "ftn" is a sort of interface to other compilers, 
either Cray Fortran (crayftn), Intel (ifort), or NVidia (pgf90 and now 
nvfortran). Very confusing, especially for "configure"


Paolo

On 24/05/2023 09:28, Ivan Carnimeo wrote:

Hi,
from the configure line you reported it seems you are using ftn compiler 
(F90=ftn MPIF90=ftn) with cuda taken from nvhpc 
(--with-cuda=/opt/nvidia/hpc_sdk/Linux_x86_64/22.7/cuda)...


Ivan




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Today's Topics:

    1. [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched
   directive (Siwakorn Sukharom)
    2. Re: [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched
   directive (Paolo Giannozzi)
    3. Re: [QE-GPU] compilation issue : NVFORTRAN-F-1225-Unmatched
   directive (Siwakorn Sukharom)
    4. R: [QE-GPU] compilation issue :   NVFORTRAN-F-1225-Unmatched
   directive (Pietro Davide Delugas)


--

Message: 1
Date: Tue, 23 May 2023 04:47:25 +
From: Siwakorn Sukharom 
To: "users@lists.quantum-espresso.org"
     
Subject: [QE-users] [QE-GPU] compilation issue :
     NVFORTRAN-F-1225-Unmatched  directive
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

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 
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1HfVtuRXsburug_Ks6wcsSDwrA6m0QHaH%2Fview%3Fusp%3Dsharing=05%7C01%7Cpaolo.giannozzi%40uniud.it%7Cb3334e6e6c19420adc7608db5c287d1a%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638205101230739304%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=uuHcgak3%2BZ%2Bqnvf2TgBRYe6pKzVqxV45fLL6fVlt%2Bg8%3D=0>


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/ins

  tall/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?

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

[Paolo Giannozzi]

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 make.inc 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



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

[Paolo Giannozzi]

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
___
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

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

[Paolo Giannozzi]

On 23/05/2023 06:47, Siwakorn Sukharom wrote:


/NVFORTRAN-F-1225-Unmatched directive END - DATA. (drhoc_tmp.f90: 90)/
/NVFORTRAN/x86-64 Linux 22.7-0: compilation aborted/


go to line 90 of PW/src/drhoc_tmp.f90 and see what is wrong there

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