[Pw_forum] Tetrahedron and alpha2f.x problem

Mitsuaki Kawamura mkawamura at issp.u-tokyo.ac.jp
Sun Sep 17 16:01:33 CEST 2017


Dear Dr. Uzunok

This is the bug of the new XML routine.
https://github.com/QEF/q-e/commit/b64d4f587e4fe960eeaaf4743f81dd73b5901e37#diff-93187c5c1813e8209c7f5f77f307d759

I attached the patch file of this bug-fix commit.
Please apply this file at the top directory of QE as follows:
$ patch -p1 < patch.diff

Best regards,
Mitsuaki Kawamura

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Huseyin Yasin Uzunok
Sent: Sunday, September 17, 2017 7:54 PM
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] Tetrahedron and alpha2f.x problem

Dr. Mitsuaki Kawamura,

When I choose  tetrahedron occupation, it strangely changed my celldm3 parameter for tetragonal structure in phonon calculation after the scf calculation. In SCF.out file it is written as;

  celldm(1)=   8.592849  celldm(2)=   0.000000  celldm(3)=   2.257000
     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000

for my cell parameters. But in the ph.out file it is written as;

celldm(1)=    8.59285  celldm(2)=    0.00000  celldm(3)=    9.69703
     celldm(4)=    0.00000  celldm(5)=    0.00000  celldm(6)=    0.00000

What could cause this, do you have any idea? My input file is as follows;


******************************************************************************************************************
#!/bin/sh
export CPUNUMBER=24

cat > scf.in << EOF
SrPtGe3
SrPtGe3
 &control
    calculation='scf'
    restart_mode='from_scratch',
    tstress = .true.
    tprnfor = .true.
    prefix='SrPtGe3',
    pseudo_dir ='$HOME/espresso-5.2.1/pseudo/',
    outdir='$HOME/murx/SrPtGe3/',
 /
 &system
    ibrav= 7,
    celldm(1)=   8.592849,
    celldm(3)=   2.257000,
    nat= 5, ntyp= 3,
    ecutwfc= 60.0,
    ecutrho= 480.0,
    occupations='tetrahedra_opt',
/
 &electrons
/
ATOMIC_SPECIES
Sr    87.62000      Sr.pbe-spn-rrkjus_psl.0.2.3.UPF
Pt    195.0780      Pt.pbe-n-rrkjus_psl.0.1.UPF
Ge    72.61000      Ge.pbe-dn-rrkjus_psl.0.2.2.UPF
ATOMIC_POSITIONS {crystal}
Sr       0.000000000   0.000000000   0.000000000
Pt       0.000000000   0.643586498   0.643586498
Ge       0.000000000   0.400158073   0.400158073
Ge      -0.500000000   0.754094097   0.254094097
Ge       0.500000000   0.254094097  -0.245905903
K_POINTS automatic
8 8 8  0 0 0
EOF

mpirun -np $CPUNUMBER -machinefile ./nodes $HOME/qe-6.1/bin/pw.x  $PARA_POSTFIX < scf.in > SCF.out 2>&1

cat > ph.in << EOF
Phonons in SrPtGe3
&INPUTPH
   prefix = 'SrPtGe3',
   outdir = '$HOME/murx/SrPtGe3/',
   fildyn = 'SrPtGe3.dyn'
 fildvscf = 'dv',
  fildrho = 'drho',
    ldisp = .true.,
 lshift_q = .false.,
      nq1 = 2,
      nq2 = 2,
      nq3 = 2,
/
EOF

mpirun -np $CPUNUMBER -machinefile ./nodes $HOME/qe-6.1/bin/ph.x  $PARA_POSTFIX < ph.in > ph.out 2>&1


cat > elph.in << EOF
Electron-phonon in SrPtGe3
&INPUTPH
          prefix = 'SrPtGe3',
          outdir = '$HOME/murx/SrPtGe3/',
          fildyn = 'SrPtGe3.dyn'
        fildvscf = 'dv',
         fildrho = 'drho',
           ldisp = .true.,
        lshift_q = .false.,
             nq1 = 2,
             nq2 = 2,
             nq3 = 2,
 electron_phonon = "lambda_tetra"
             nk1 = 16,
             nk2 = 16,
             nk3 = 16,
/
EOF


mpirun -np $CPUNUMBER -machinefile ./nodes $HOME/qe-6.1/bin/ph.x  $PARA_POSTFIX < elph.in > elph.out 2>&1

***********************************************************************************************************************************************************
thanks in advance.


2017-09-16 17:18 GMT+03:00 Hüseyin Yasin Uzunok <hyuzunok at sakarya.edu.tr>:
Thank you very much for your help. Have a nice day.

2017-09-16 16:45 GMT+03:00 Mitsuaki Kawamura <mkawamura at issp.u-tokyo.ac.jp>:
Dera Dr. UZUNOK

The reference output is also modified.
https://github.com/QEF/q-e/tree/master/PHonon/examples/tetra_example/reference

Best regards,
Mitsuaki Kawamura

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Huseyin Yasin Uzunok
Sent: Saturday, September 16, 2017 7:13 PM
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: Re: [Pw_forum] Tetrahedron and alpha2f.x problem

Thank you Dr. Mitsuaki Kawamura. New input was quite a help. But it does not gave the same results in the references file. it it normal?

2017-09-16 8:13 GMT+03:00 Mitsuaki Kawamura <mkawamura at issp.u-tokyo.ac.jp>:
Dear Dr. UZUNOK

Hello,

I am sorry, the input-file format of alpha2f.x program was modified and the script for the example does not work correctly.
The correct run_example script is included in the developing version of QE. It is available here:

https://github.com/QEF/q-e/blob/master/PHonon/examples/tetra_example/run_example

I am sorry for the inconvenience.

Best regards,
Mitsuaki Kawamura

--
------------------------------------------------------
Dr. Mitsuaki Kawamura
Software Advancement Team
Supercomputer Section
Materials Design and Characterization Laboratory
The Institute for Solid State Physics, Kashiwa, Japan
e-mail : mkawamura at issp.u-tokyo.ac.jp
------------------------------------------------------

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Huseyin Yasin Uzunok
Sent: Saturday, September 16, 2017 3:18 AM
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: [Pw_forum] Tetrahedron and alpha2f.x problem

Dear QE community,

I have tried to run tetra_example in the qe-6.1/Examples/PHonon directory for Aluminum. At first in the phonon calculation, it gave an error. So I recompiled it as suggested in this link;

http://qe-forge.org/pipermail/pw_forum/2017-April/112600.html

With this, I can able to do phonon and electron phonon calculations with tetrahedron occupation. But I could not able to run alpha2f.x execution. I follow the suggestions and I found this entry;


http://qe-forge.org/pipermail/pw_forum/2017-April/112604.html

I took the files in the links and tried to recompile the PHonon. (By the way, In the "Makefile" there is an UtilXlib that normally noy included. ı have found it at the internet but it was no use.) I have compiled the alpha2f.x and tried the tetre_example again. I have an error massage as follow;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from phq_readin : error #         1
     reading inputph namelist
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Is this error caused by the phq_readin.f90 or is it about my executable file? Thanks in advance.
--
-----------------------------------------------------------
Arş. Gör. H. Y. UZUNOK
Sakarya Üniversitesi Fizik Bölümü
Tel:+90 264 2956192
Gsm: +90 554 7300135
--------------------------------------------------

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--
-----------------------------------------------------------
Arş. Gör. H. Yasin UZUNOK
Sakarya Üniversitesi Fizik Bölümü
Tel:+90 264 2956192
Gsm: +90 554 7300135
--------------------------------------------------


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum




-- 
-----------------------------------------------------------
Arş. Gör. H. Yasin UZUNOK
Sakarya Üniversitesi Fizik Bölümü
Tel:+90 264 2956192
Gsm: +90 554 7300135
--------------------------------------------------




-- 
-----------------------------------------------------------
Arş. Gör. H. Yasin UZUNOK
Sakarya Üniversitesi Fizik Bölümü
Tel:+90 264 2956192
Gsm: +90 554 7300135
--------------------------------------------------
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