[QE-users] Installation of QE in cluster based server remotely

[vipin kumar]

Dear All,

   I am having account in IUAC super-computing facility and
accessing from my desktop using SSH and trying to install in my account.
Anyone can suggest how to install it?

Thank you

Regards,
Vipin
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[QE-users] Calculating formation energy of the defect

[mehrdad zamzamian]

Hi all dear QE users
I'm working on the formation energy of a single Fe vacancy in Fe3C
(cementite). It seems that we can calculate this parameter by:
Eform=EFe31−xCtot–EFe3Ctot+x⋅EFetot,
where the first term is the total energy of Fe3C with a Fe vacancy, the
second one is the total energy of Fe3C (without defect) and the 3rd one is
the total energy of a single Fe. x for this case can be 1 because we have a
Fe vacancy. Is this a correct way to calculate?
the second problem is the scf calculation does not converge and begins to
fail after almost 75 iterations (see figure) for the case of pure Fe (when
i want to calculate Fe-vacancy in BCC-Fe). These conditions also exist for
optimization, i can reach neither to convergence for scf nor to an
optimized geometry. Here is my input.

[image: BCC-Fe3.png]

calculation = "scf"
max_seconds =  8.64000e+04
pseudo_dir  = "C:\Users\pseudo"
/
a =  5.03018e+00
b =  6.73931e+00
c =  4.49084e+00
degauss   =  1.0e-02
ecutrho   =  2.25000e+02
ecutwfc   =  2.5e+01
ibrav = 8
nat   = 16
nspin = 2
ntyp  = 2
occupations   = "smearing"
smearing  = "gaussian"
starting_magnetization(1) =  2.0e-01
starting_magnetization(2) =  0.0e+00
/


conv_thr =  1.0e-06
electron_maxstep = 200
mixing_beta  =  4.0e-01
startingpot  = "atomic"
startingwfc  = "atomic+random"
/

K_POINTS {automatic}
 2  2  3  0 0 0

ATOMIC_SPECIES
Fe 55.84500  Fe.pbe-nd-rrkjus.UPF
C  12.01070  C.pbe-rrkjus.UPF

ATOMIC_POSITIONS {angstrom}
Fe  0.892203   0.460793   1.491414
Fe  4.137977   6.278514   2.999431
Fe  1.622887   6.278514   3.736836
Fe  3.407293   0.460793   0.754008
Fe  3.407293   2.908860   0.754008
Fe  1.622887   3.830447   3.736836
Fe  4.137977   3.830447   2.999431
Fe  0.892203   2.908860   1.491414
Fe  0.184411   1.684827   3.759376
Fe  4.845769   5.054480   0.731469
Fe  2.330679   5.054480   1.513954
Fe  2.699502   1.684827   2.976891
C   0.618742   5.054480   2.519058
C   4.411438   1.684827   1.971786
C   1.896348   1.684827   0.273636
C   3.133833   5.054480   4.217209


Thanks in advance
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Re: [QE-users] 2D band surface plot

[Oleksandr Motornyi]

Hello Eleni

Could you please provide an input as well as the strange outputs? It is 
hard to give any advice or example without knowing what are you dealing 
with exactly.


Regards,

Oleksandr

Oleksandr Motornyi
PhD

Laboratoire des Solides Irradies
Ecole Polytechnique (Palaiseau, France)

On 29/04/19 18:12, elch...@auth.gr wrote:

Hello everyone,

Do you have an example with a grid used for 2D surface plot in 
bands.x? I am getting some really strange output.


Regards,

Eleni




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[QE-users] 2D band surface plot

[elchatz]

Hello everyone,

Do you have an example with a grid used for 2D surface plot in  
bands.x? I am getting some really strange output.


Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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[QE-users] scan with paw

[jiayu]

of OpenMPI
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi,
> I would like to install QE with a non default MPI version on my cluster. I
> have installed it in /share/apps/qe-6.4 and MPI is in
> /share/apps/openmpi-4.0.1
> 
> It seems that I can only set env variables such as CC and ...
> Is that enough?
> 
> Regards,
> Mahmood
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> <http://lists.quantum-espresso.org/pipermail/users/attachments/20190428/07a5400d/attachment-0001.html>
> 
> --
> 
> Message: 4
> Date: Sun, 28 Apr 2019 21:19:27 +0200
> From: Mohamed Ahmed Abd-Elati 
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] installation QE with mpi
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear QE developers and users
> I am installed QE and *When I run it using 1 core  no issues occur, but
> when *
> * more than 1 core  using  on my 40 core machine (mpirun -np 10
> /media/mohamed/5E2B53A447660601/QE-Code/q-e-qe-6.4.1/bin/pw.x
> <5x5-H.relax.in <http://5x5-H.relax.in>> 5x5-H.relax.out ) I am faced the
> following error.*
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> *STOP 1from test_input_xml: input file not opened or emptySTOP 1from
> test_input_xml: input file not opened or emptySTOP 1from test_input_xml:
> input file not opened or emptySTOP 1from test_input_xml: input file not
> opened or emptySTOP 1from test_input_xml: input file not opened or
> emptySTOP 1from test_input_xml: input file not opened or emptySTOP 1from
> test_input_xml: input file not opened or emptySTOP
> 1.*
> *I am trying many times to do all instructions in this link
> (https://lists.quantum-espresso.org/pipermail/users/2018-August/041134.html
> <https://lists.quantum-espresso.org/pipermail/users/2018-August/041134.html>
> ) but my issue still facing me.*
> *Please what can I do in details to mpirun QE.*
> 
> *Thanks in advanced*
> *Mohammed A. Abdelati*
> *Assistant Lecturer*
> Laser Applications in Metrology Photochemistry and Agriculture (LAMPA)
> Department, National Institute of Laser Enhanced Sciences (NILES), Cairo
> University, Giza, Egypt.
> Mobile   +20 1009752922
> Home+201152605076
> E-mailma198...@yahoo.com
> -- next part --
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> 
> --
> 
> Message: 5
> Date: Sun, 28 Apr 2019 22:10:10 +0200
> From: Paolo Giannozzi 
> To: Quantum Espresso users Forum 
> Subject: Re: [QE-users] installation QE with mpi
> Message-ID:
>
> Content-Type: text/plain; charset="utf-8"
> 
> On Sun, Apr 28, 2019 at 9:19 PM Mohamed Ahmed Abd-Elati 
> wrote:
> 
> *mpirun -np 10
>> /media/mohamed/5E2B53A447660601/QE-Code/q-e-qe-6.4.1/bin/pw.x
>> <5x5-H.relax.in <http://5x5-H.relax.in>> 5x5-H.relax.out*
>> 
> 
> try first of all "-in 5x5-H.relax.in" instead of "< 5x5-H.relax.in"
> 
> P.
> -- 
> 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
> -- next part --
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> 
> --
> 
> Message: 6
> Date: Mon, 29 Apr 2019 11:26:01 +0800 (CST)
> From: "Hao Gao" 
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] Calculate el-ph interactions from external IFCs
> Message-ID: <237d06c6.3060.16a6720c4f0.coremail.gaa...@126.com>
> Content-Type: text/plain; charset="gbk"
> 
> Dear all,
> 
> 
> I have obtained anharmonic 2nd-order IFCs using Linear Regression in 
> phonopy's format. Then how can I calculate el-ph interactions using the IFCs 
> by QE?
> 
> I find I. Errea, et al have calulated anharmonic Tc by QE in Phys. Rev. Lett. 
> 114, 157004 (2015). Is there some guidance on this issue?
> 
> Thank you.
> 
> 
> Hao Gao
> Nanjing University
> -- next part --
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> 
> --
> 
> Message: 7
> Date: Mon, 29 Apr 2019 09:26:39 +0200
&g

[QE-users] Config for pseudopotential generation

[Pamela Svensson]

Hi all,


I am a beginner at QE and want to generate a pseudopotential with ld1.x but 
have difficulties understanding the config keyword.

Why does gipaw occupation for C obtained at the QE homepage 
(C.pbe-mt_gipaw.UPF) have config=2s2 2p1.5 but for others such as kjpaw etc 
have config=2s2 2p2?


Also, what config is recommended for generating a gipaw PP for N?


Thanks

Pamela








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[QE-users] Format of filp output file in bands.x

[elchatz]

Hello everyone,

Is there a guide on the format of the filp file in the bands.x  
calculation for me to parse it?



Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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[QE-users] Installation verification

[Mahmood Naderan]

Hi
I want to know if I have correctly built qe with openmpi-4.0. So, I ran the
following command and got this error

[root@rocks7 q-e-qe-6.4]# ./configure
--prefix=/share/apps/softwares/q-e-qe-6.4
MPIF90=/share/apps/softwares/openmpi-4.0.1/bin/mpif90
...
[root@rocks7 q-e-qe-6.4]# make all
...
[mahmood@rocks7 job]$ /share/apps/softwares/openmpi-4.0.1/bin/mpirun
/share/apps/softwares/q-e-qe-6.4/bin/pw.x
--
As of version 3.0.0, the "sm" BTL is no longer available in Open MPI.

Efficient, high-speed same-node shared memory communication support in
Open MPI is available in the "vader" BTL.  To use the vader BTL, you
can re-run your job with:

mpirun --mca btl vader,self,... your_mpi_application
--
--
A requested component was not found, or was unable to be opened.  This
means that this component is either not installed or is unable to be
used on your system (e.g., sometimes this means that shared libraries
that the component requires are unable to be found/loaded).  Note that
Open MPI stopped checking at the first component that it did not find.

Host:  rocks7.jupiterclusterscu.com
Framework: btl
Component: sm
--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  mca_bml_base_open() failed
  --> Returned "Not found" (-13) instead of "Success" (0)
--
[rocks7:19796] *** An error occurred in MPI_Init
[rocks7:19796] *** reported by process [85917697,3255307776955514882]
[rocks7:19796] *** on a NULL communicator
[rocks7:19796] *** Unknown error
[rocks7:19796] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
will now abort,
[rocks7:19796] ***and potentially your MPI job)
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in file
server/pmix_server.c at line 2079
[rocks7.jupiterclusterscu.com:19784] PMIX ERROR: UNREACHABLE in 

Re: [QE-users] Calculate el-ph interactions from external IFCs

[Lorenzo Paulatto]

Dear Hao,
you need to convert the IFCs to quantum-espresso format if you want to 
use them in QE. Some time ago I wrote a python script that can do this 
conversion, it is part of the d3q code, but you can get it just the 
script here:



PLEASE READ  THE DOCUMENTATION AT THE BEGINNING OF THE FILE!

I find I. Errea, et al have calulated anharmonic Tc by QE in Phys. Rev. 
Lett. 114, 157004 (2015). Is there some guidance on this issue?


As far as I know, Ion Errea used its own code implementing the 
Self-Consistent Harmonic Approximation. I don't know if he read this 
list, but for sure you can contact him directly.


kind regards



Thank you.

Hao Gao
Nanjing University



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--
Lorenzo Paulatto - Paris
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