date:20170917

Re: [Pw_forum] Pw_forum Digest, Vol 122, Issue 16

2017-09-17 Thread Lorenzo Paulatto

When answering to a daily sigest, please do not quote the entire 25 
pages of text, just trim down what is necessary

On 17/09/17 14:25, Phanikumar Pentyala wrote:

Thankyou Lorenzo Paulatto for your comments

Here I am giving more clarifications and doubts

commnet2: In spin polarized calculation it was asking 
starting_magnitization value. So can please tell me how to choose that 
value for CeO2 ??


It is a starting magnetization, the value does not matter. However, if 
you start from something closer to the final value, it will converge 
faster. Please check the manual:





comment1: System was CeO2(111) face plane

comment3: Yes. I saw so many posts saying about NORM conserving psudo 
potential. So either I will change PPs or increase ecutwfc


You must test convergence, independently from the kind of pseudos you use.



comment4: I will do search regarding this



--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05

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Re: [Pw_forum] Tetrahedron and alpha2f.x problem

2017-09-17 Thread Mitsuaki Kawamura

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-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Huseyin Yasin Uzunok
Sent: Sunday, September 17, 2017 7:54 PM
To: PWSCF Forum 
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)=   0.00  celldm(3)=   2.257000
 celldm(4)=   0.00  celldm(5)=   0.00  celldm(6)=   0.00

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

celldm(1)=8.59285  celldm(2)=0.0  celldm(3)=9.69703
 celldm(4)=0.0  celldm(5)=0.0  celldm(6)=0.0

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
 
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='SrPtGe3',
pseudo_dir ='$HOME/espresso-5.2.1/pseudo/',
outdir='$HOME/murx/SrPtGe3/',
 /
 
ibrav= 7,
celldm(1)=   8.592849,
celldm(3)=   2.257000,
nat= 5, ntyp= 3,
ecutwfc= 60.0,
ecutrho= 480.0,
occupations='tetrahedra_opt',
/
 
/
ATOMIC_SPECIES
Sr87.62000  Sr.pbe-spn-rrkjus_psl.0.2.3.UPF
Pt195.0780  Pt.pbe-n-rrkjus_psl.0.1.UPF
Ge72.61000  Ge.pbe-dn-rrkjus_psl.0.2.2.UPF
ATOMIC_POSITIONS {crystal}
Sr   0.0   0.0   0.0
Pt   0.0   0.643586498   0.643586498
Ge   0.0   0.400158073   0.400158073
Ge  -0.5   0.754094097   0.254094097
Ge   0.5   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

   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

  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 :
Thank you very much for your help. Have a nice day.

2017-09-16 16:45 GMT+03:00 Mitsuaki Kawamura :
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-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On Behalf 
Of Huseyin Yasin Uzunok
Sent: Saturday, September 16, 2017 7:13 PM
To: PWSCF Forum 
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 :
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 : mkawam...@issp.u-tokyo.ac.jp

[Pw_forum] wannier_ham /CRASH

2017-09-17 Thread nazari

 Dear All,
  The wannier_ham.x code terminated by the following error. The inputs and
outputs are in the attachment. Would you please let we know the
solution?

regards
Fariba
IASBS

 # forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLineSource
wannier_ham.x  004998DD  wannier_check_ 36 
wannier_check.f90
wannier_ham.x  0049909F  wannier_init_  55 
wannier_init.f90
wannier_ham.x  0044392E  MAIN__ 70 
wannier_ham.f90
wannier_ham.x  0044385C  Unknown   Unknown  Unknown
libc.so.6  003B01E1ECDD  Unknown   Unknown  Unknown
wannier_ham.x  00443759  Unknown   Unknown  Unknown


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



scf.in
Description: Binary data


wan.in
Description: Binary data


wout.out
Description: Binary data
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Re: [Pw_forum] Tetrahedron and alpha2f.x problem

2017-09-17 Thread Hüseyin Yasin Uzunok

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)=   0.00  celldm(3)=   2.257000
 celldm(4)=   0.00  celldm(5)=   0.00  celldm(6)=   0.00

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

celldm(1)=8.59285  celldm(2)=0.0  celldm(3)=9.69703
 celldm(4)=0.0  celldm(5)=0.0  celldm(6)=0.0

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
 
calculation='scf'
restart_mode='from_scratch',
tstress = .true.
tprnfor = .true.
prefix='SrPtGe3',
pseudo_dir ='$HOME/espresso-5.2.1/pseudo/',
outdir='$HOME/murx/SrPtGe3/',
 /
 
ibrav= 7,
celldm(1)=   8.592849,
celldm(3)=   2.257000,
nat= 5, ntyp= 3,
ecutwfc= 60.0,
ecutrho= 480.0,
occupations='tetrahedra_opt',
/
 
/
ATOMIC_SPECIES
Sr87.62000  Sr.pbe-spn-rrkjus_psl.0.2.3.UPF
Pt195.0780  Pt.pbe-n-rrkjus_psl.0.1.UPF
Ge72.61000  Ge.pbe-dn-rrkjus_psl.0.2.2.UPF
ATOMIC_POSITIONS {crystal}
Sr   0.0   0.0   0.0
Pt   0.0   0.643586498   0.643586498
Ge   0.0   0.400158073   0.400158073
Ge  -0.5   0.754094097   0.254094097
Ge   0.5   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

   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

  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 :

> Thank you very much for your help. Have a nice day.
>
> 2017-09-16 16:45 GMT+03:00 Mitsuaki Kawamura  >:
>
>> 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-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On
>> Behalf Of Huseyin Yasin Uzunok
>> Sent: Saturday, September 16, 2017 7:13 PM
>> To: PWSCF Forum 
>> 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 > >:
>> 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 : mkawam...@issp.u-tokyo.ac.jp
>> --
>>
>> From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On
>> Behalf Of Huseyin Yasin Uzunok
>> Sent: Saturday, September 16, 2017 3:18 AM
>> To: PWSCF Forum 
>> 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
>>

[Pw_forum] unsubscription

2017-09-17 Thread Maha Alattas

Good day,
I would like to end my subscription in the forum.

Thank you for your time. Have a good one.



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M: (+966) 5363-858-15
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Re: [Pw_forum] Role of awin for macroscopic average calculation

2017-09-17 Thread shashi bhusan mishra

Thanks a lot Paolo. I got clear idea of the input description.


Thanks and regards,

‌  Shashi

Shashi Bhusan Mishra
Research Scholar,
Dept. Of Physics,
Room No- HSB209A
IIT Madras-36

On Sun, Sep 17, 2017 at 1:11 AM, Paolo Giannozzi 
wrote:

> An improved documentation of average.x can be found in the header of the
> development version of  file PP/src/average.f90:
> https://github.com/QEF/q-e/blob/master/PP/src/average.f90
>
> Paolo
>
> On Sat, Sep 16, 2017 at 9:11 PM, shashi bhusan mishra <
> mshashi...@gmail.com> wrote:
>
>> Dear QE users,
>>
>>   I have a query regarding calculation of macroscopic and planar
>> average potential. While creating the input for average potential, what is
>> the role of the term *awin* ( the size of the window for macroscopic
>> averages). Can anyone give some more detail about the role of awin term and
>> how to choose suitable size ?
>>In addition to that while calculating the planar average, though I
>>  specified nx,ny and nz values, the program sets automatic mesh grid size.
>> Is it automatic or user specified ? The file format is shown below:
>>
>> outdir='/',
>> plot_num=11
>> filplot = 'test.pot'
>> /   
>>iflag=3,
>>   output_format=3
>>nx=51,ny=51,nz= 121
>>/
>> and averge input file:
>> 1
>> filename
>> 1.0
>> 3000
>> 3
>> 2.59
>>
>> Thanks in advance.
>>
>>
>>
>> Thanks and regards,
>>
>> Shashi Bhusan Mishra
>> Research Scholar,
>> Dept.
>> o
>> f Physics,
>> Room No- HSB209A
>> IIT Madras-36
>>
>>
>>
>>  Sent with Mailtrack
>> 
>>
>> ___
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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: [Pw_forum] Pw_forum Digest, Vol 122, Issue 16

Re: [Pw_forum] Tetrahedron and alpha2f.x problem

[Pw_forum] wannier_ham /CRASH

Re: [Pw_forum] Tetrahedron and alpha2f.x problem

[Pw_forum] unsubscription

Re: [Pw_forum] Role of awin for macroscopic average calculation

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