date:20160202

Re: [Pw_forum] coefficients of plane wave

2016-02-02 Thread Eliya Asmani

Thanks so much. I try it.

Best

On Wed, Feb 3, 2016 at 2:14 AM, Jia Chen  wrote:

> When you run pw.x, use commend like that: pw.x -pw2casino
> Moreover, you need a file named pw2casino.dat in current directory.
> In that file, you would have something like following if you would like
> coefficient in text format
> &inputpp
> blip_convert=.false.
> blip_binary=.false.
> blip_single_prec=.false.
> blip_multiplicity=1.d0
> n_points_for_test=0
> /
> After, you will find coefficients in a large file named prefix.pwfn.data
> You also can find details about pw2casino in the manual of casino.
>
> Cheers
> Jia
>
> On Tue, Feb 2, 2016 at 5:02 PM, Eliya Asmani  wrote:
>
>> Thanks, but I need them in reciprocal space.
>> Can you explain me more about pw2casino?
>>
>> On Wed, Feb 3, 2016 at 1:20 AM, Lorenzo Paulatto <
>> lorenzo.paula...@impmc.upmc.fr> wrote:
>>
>>> You can also use the tool wfck2r.x from the PP directory, which would
>>> write
>>> out the wavefunctions in real space
>>>
>>>
>>>
>>> --
>>> Dr. Lorenzo Paulatto
>>> IdR @ IMPMC -- CNRS & Université Paris 6
>>> +33 (0)1 44 275 084 / skype: paulatz
>>> http://www.impmc.upmc.fr/~paulatto/
>>> 23-24/4é16 Boîte courrier 115
>>> 4 place Jussieu 75252 Paris Cédex 05
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
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>
>
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Re: [Pw_forum] coefficients of plane wave

2016-02-02 Thread Jia Chen

When you run pw.x, use commend like that: pw.x -pw2casino
Moreover, you need a file named pw2casino.dat in current directory.
In that file, you would have something like following if you would like
coefficient in text format
&inputpp
blip_convert=.false.
blip_binary=.false.
blip_single_prec=.false.
blip_multiplicity=1.d0
n_points_for_test=0
/
After, you will find coefficients in a large file named prefix.pwfn.data
You also can find details about pw2casino in the manual of casino.

Cheers
Jia

On Tue, Feb 2, 2016 at 5:02 PM, Eliya Asmani  wrote:

> Thanks, but I need them in reciprocal space.
> Can you explain me more about pw2casino?
>
> On Wed, Feb 3, 2016 at 1:20 AM, Lorenzo Paulatto <
> lorenzo.paula...@impmc.upmc.fr> wrote:
>
>> You can also use the tool wfck2r.x from the PP directory, which would
>> write
>> out the wavefunctions in real space
>>
>>
>>
>> --
>> Dr. Lorenzo Paulatto
>> IdR @ IMPMC -- CNRS & Université Paris 6
>> +33 (0)1 44 275 084 / skype: paulatz
>> http://www.impmc.upmc.fr/~paulatto/
>> 23-24/4é16 Boîte courrier 115
>> 4 place Jussieu 75252 Paris Cédex 05
>>
>>
>> ___
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>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
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Re: [Pw_forum] coefficients of plane wave

2016-02-02 Thread Eliya Asmani

Thanks, but I need them in reciprocal space.
Can you explain me more about pw2casino?

On Wed, Feb 3, 2016 at 1:20 AM, Lorenzo Paulatto <
lorenzo.paula...@impmc.upmc.fr> wrote:

> You can also use the tool wfck2r.x from the PP directory, which would write
> out the wavefunctions in real space
>
>
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www.impmc.upmc.fr/~paulatto/
> 23-24/4é16 Boîte courrier 115
> 4 place Jussieu 75252 Paris Cédex 05
>
>
> ___
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>
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Re: [Pw_forum] coefficients of plane wave

2016-02-02 Thread Lorenzo Paulatto

You can also use the tool wfck2r.x from the PP directory, which would write 
out the wavefunctions in real space



-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115
4 place Jussieu 75252 Paris Cédex 05


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Re: [Pw_forum] So many atomic wfc

2016-02-02 Thread Paolo Giannozzi

Well, no, line 412 and following (noncolinear/spinorbit case); line 161 and
following is the standard case, in which it is unlikely to have more than
10 atomic wavefunctions

Paolo

On Tue, Feb 2, 2016 at 9:40 PM, Paolo Giannozzi 
wrote:

> On Tue, Feb 2, 2016 at 1:11 PM, Hüseyin Yasin Uzunok <
> hyuzu...@sakarya.edu.tr> wrote:
>
>>  from partialdos_nc : error #31
>>  file extension not supporting so many atomic wfc
>>
>> I guess that the problem is upcoming from the number of allowed wfc
>>
>
> no, it is a rather dumb problem with file names and formats. You have to
> modify this part (line 161 and following in PP/src/partialdos.f90):
> WRITE (filextension(c_tab:),'(")_wfc#",i1,"(",a1,")")')  &
>  nlmchi(nwfc)%n, l_label(nlmchi(nwfc)%l)
> to account for the case nlmchi(nwfc)%n > 9 (note the format i1)
>
> Paolo
> --
> 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: [Pw_forum] Phonon_Calculations

2016-02-02 Thread Mofrad, Amir Mehdi (MU-Student)

If you mean like mpirun then yes.


Amir M. Mofrad




From: pw_forum-boun...@pwscf.org  on behalf of 
Paolo Giannozzi 
Sent: Tuesday, February 2, 2016 2:30 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Phonon_Calculations

Has your machine a parallel file system?

Paolo

On Tue, Feb 2, 2016 at 5:35 PM, Mofrad, Amir Mehdi (MU-Student) 
mailto:am...@mail.missouri.edu>> wrote:
Thank you for your reply Dr. Paulatto. The problem is that I used to run the 
same type of calculation (scf first and then phonon calculation) on my personal 
computers and never had got this error (I got other errors which I was able to 
solve). However, when I try to do this calculation on a cluster it gives me the 
error that I mentioned in the previous email. In order to be clear, I put the 
input files of both scf and phonon calculations here:

SCF INPUT:

&CONTROL
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  wf_collect = .true. ,
  outdir = './scratch' ,
  wfcdir = './scratch' ,
  pseudo_dir = '../../../pseudo' ,
  prefix = 'LTA' ,
   verbosity = 'high' ,
   etot_conv_thr = 1e-5 ,
   forc_conv_thr = 1e-4 ,
   nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,
 /

 &SYSTEM
   ibrav = 0,
 nat =72 ,
ntyp = 2,
 ecutwfc = 90 ,
 ecutrho = 360 ,
 /

 &ELECTRONS
electron_maxstep = 100,
conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.7 ,
 diagonalization = 'david' ,
/


CELL_PARAMETERS angstrom

  11.91900   0.0   0.0
  0.0  11.91900   0.0
  0.0   0.0  11.91900
ATOMIC_SPECIES
Si   28.08600  Si.pz-hgh.UPF
O   15.99940  O.pz-hgh.UPF

ATOMIC_POSITIONS angstrom
 O  -0.0   2.52921   5.95950
 O   1.31467   1.31467   4.03339
 O  -0.0   3.53637   3.53637
Si  -0.0   2.17283   4.39096
 O  -0.0   9.38979   5.95950
 O   5.95950  -0.0   2.52921
 O   5.95950  -0.0   9.38979
 O   2.52921   5.95950   0.0
 O   9.38979   5.95950   0.0
 O   2.52921  -0.0   5.95950
 O   9.38979  -0.0   5.95950
 O  -0.0   5.95950   9.38979
 O  -0.0   5.95950   2.52921
 O   5.95950   2.52921   0.0
 O   5.95950   9.38979   0.0
 O  10.60433  10.60433   4.03339
 O  10.60433   1.31467   7.88561
 O   1.31466  10.60433   7.88561
 O   4.03339   1.31467   1.31467
 O   4.03339  10.60433  10.60433
 O   7.88561  10.60433   1.31467
 O   7.88561   1.31467  10.60433
 O   1.31467   4.03339   1.31467
 O  10.60433   4.03339  10.60433
 O   1.31466   7.88561  10.60433
 O  10.60433   7.88561   1.31467
 O   1.31467   1.31467   7.88561
 O  10.60433  10.60433   7.88561
 O   1.31466  10.60433   4.03339
 O  10.60433   1.31467   4.03339
 O   1.31467   4.03339  10.60433
 O  10.60433   4.03339   1.31467
 O  10.60433   7.88561  10.60433
 O   1.31467   7.88561   1.31467
 O   4.03339   1.31467  10.60433
 O   4.03339  10.60433   1.31467
 O   7.88561   1.31467   1.31467
 O   7.88561  10.60433  10.60433
 O  -0.0   8.38263   3.53637
 O  -0.0   3.53637   8.38263
 O  -0.0   8.38263   8.38263
 O   3.53637  -0.0   3.53637
 O   3.53637  -0.0   8.38263
 O   8.38263  -0.0   3.53637
 O   8.38263  -0.0   8.38263
 O   3.53637   3.53637   0.0
 O   8.38263   3.53637   0.0
 O   3.53637   8.38263   0.0
 O   8.38263   8.38263   0.0
Si  -0.0   9.74617   4.39096
Si  -0.0   2.17283   7.52804
Si  -0.0   9.74617   7.52804
Si   4.39096  -0.0   2.17283
Si   4.39096  -0.0   9.74617
Si   7.52804  -0.0   2.17283
Si   7.52804  -0.0   9.74617
Si   2.17283   4.39096   0.0
Si   9.74617   4.39096   0.0
Si   2.17283   7.52804   0.0
Si   9.74617   7.52804   0.0
Si   2.17283  -0.0   7.52804
Si   9.74617  -0.0   7.52804
Si   2.17283  -0.0   4.39096
Si   9.74617  -0.0   4.39096
Si  -0.0   4.39096   9.74617
Si  -0.0   4.39096   2.17283
Si  -0.0   7.52804   9.74617
Si  -0.0   7.52804   2.17283
Si   4.39096   2.17283   0.0
Si   4.39096   9.74617   0.0
Si   7.52804   2.17283   0.0
Si   7.52804   9.74617   0.0
K_POINTS automatic
4 4 4 1 1 1


PHONON INPUT

normal modes for LTA
 &inputph
 tr2_ph=1.0d-14,
 prefix='LTA',
 epsil=.true.,
 fildyn='LTA.dyn'
 outdir='./scratch',
 trans=.true.,
 lraman=.true.,
/
0.0 0.0 0.0


Best regards,

Amir M. Mofrad



From: pw_forum-boun...@pwscf.org 
mailto:pw_forum-boun...@pwscf.org>> on behalf of 
Lorenzo Paulatto 
mailto:lorenzo.paula...@impmc.upmc.fr>>
Sent: Tuesday, February 2, 2016 2:46 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Phonon_Calculations

On Mond

Re: [Pw_forum] So many atomic wfc

2016-02-02 Thread Paolo Giannozzi

On Tue, Feb 2, 2016 at 1:11 PM, Hüseyin Yasin Uzunok <
hyuzu...@sakarya.edu.tr> wrote:

>  from partialdos_nc : error #31
>  file extension not supporting so many atomic wfc
>
> I guess that the problem is upcoming from the number of allowed wfc
>

no, it is a rather dumb problem with file names and formats. You have to
modify this part (line 161 and following in PP/src/partialdos.f90):
WRITE (filextension(c_tab:),'(")_wfc#",i1,"(",a1,")")')  &
 nlmchi(nwfc)%n, l_label(nlmchi(nwfc)%l)
to account for the case nlmchi(nwfc)%n > 9 (note the format i1)

Paolo
-- 
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] Phonon_Calculations

2016-02-02 Thread Paolo Giannozzi

Has your machine a parallel file system?

Paolo

On Tue, Feb 2, 2016 at 5:35 PM, Mofrad, Amir Mehdi (MU-Student) <
am...@mail.missouri.edu> wrote:

> Thank you for your reply Dr. Paulatto. The problem is that I used to run
> the same type of calculation (scf first and then phonon calculation) on my
> personal computers and never had got this error (I got other errors which I
> was able to solve). However, when I try to do this calculation on a cluster
> it gives me the error that I mentioned in the previous email. In order to
> be clear, I put the input files of both scf and phonon calculations here:
>
> SCF INPUT:
>
> &CONTROL
>  calculation = 'scf' ,
> restart_mode = 'from_scratch' ,
>   wf_collect = .true. ,
>   outdir = './scratch' ,
>   wfcdir = './scratch' ,
>   pseudo_dir = '../../../pseudo' ,
>   prefix = 'LTA' ,
>verbosity = 'high' ,
>etot_conv_thr = 1e-5 ,
>forc_conv_thr = 1e-4 ,
>nstep = 50 ,
>  tstress = .true. ,
>  tprnfor = .true. ,
>  /
>
>  &SYSTEM
>ibrav = 0,
>  nat =72 ,
> ntyp = 2,
>  ecutwfc = 90 ,
>  ecutrho = 360 ,
>  /
>
>  &ELECTRONS
> electron_maxstep = 100,
> conv_thr = 3e-8 ,
>  mixing_mode = 'plain' ,
>  mixing_beta = 0.7 ,
>  diagonalization = 'david' ,
> /
>
>
> CELL_PARAMETERS angstrom
>
>   11.91900   0.0   0.0
>   0.0  11.91900   0.0
>   0.0   0.0  11.91900
> ATOMIC_SPECIES
> Si   28.08600  Si.pz-hgh.UPF
> O   15.99940  O.pz-hgh.UPF
>
> ATOMIC_POSITIONS angstrom
>  O  -0.0   2.52921   5.95950
>  O   1.31467   1.31467   4.03339
>  O  -0.0   3.53637   3.53637
> Si  -0.0   2.17283   4.39096
>  O  -0.0   9.38979   5.95950
>  O   5.95950  -0.0   2.52921
>  O   5.95950  -0.0   9.38979
>  O   2.52921   5.95950   0.0
>  O   9.38979   5.95950   0.0
>  O   2.52921  -0.0   5.95950
>  O   9.38979  -0.0   5.95950
>  O  -0.0   5.95950   9.38979
>  O  -0.0   5.95950   2.52921
>  O   5.95950   2.52921   0.0
>  O   5.95950   9.38979   0.0
>  O  10.60433  10.60433   4.03339
>  O  10.60433   1.31467   7.88561
>  O   1.31466  10.60433   7.88561
>  O   4.03339   1.31467   1.31467
>  O   4.03339  10.60433  10.60433
>  O   7.88561  10.60433   1.31467
>  O   7.88561   1.31467  10.60433
>  O   1.31467   4.03339   1.31467
>  O  10.60433   4.03339  10.60433
>  O   1.31466   7.88561  10.60433
>  O  10.60433   7.88561   1.31467
>  O   1.31467   1.31467   7.88561
>  O  10.60433  10.60433   7.88561
>  O   1.31466  10.60433   4.03339
>  O  10.60433   1.31467   4.03339
>  O   1.31467   4.03339  10.60433
>  O  10.60433   4.03339   1.31467
>  O  10.60433   7.88561  10.60433
>  O   1.31467   7.88561   1.31467
>  O   4.03339   1.31467  10.60433
>  O   4.03339  10.60433   1.31467
>  O   7.88561   1.31467   1.31467
>  O   7.88561  10.60433  10.60433
>  O  -0.0   8.38263   3.53637
>  O  -0.0   3.53637   8.38263
>  O  -0.0   8.38263   8.38263
>  O   3.53637  -0.0   3.53637
>  O   3.53637  -0.0   8.38263
>  O   8.38263  -0.0   3.53637
>  O   8.38263  -0.0   8.38263
>  O   3.53637   3.53637   0.0
>  O   8.38263   3.53637   0.0
>  O   3.53637   8.38263   0.0
>  O   8.38263   8.38263   0.0
> Si  -0.0   9.74617   4.39096
> Si  -0.0   2.17283   7.52804
> Si  -0.0   9.74617   7.52804
> Si   4.39096  -0.0   2.17283
> Si   4.39096  -0.0   9.74617
> Si   7.52804  -0.0   2.17283
> Si   7.52804  -0.0   9.74617
> Si   2.17283   4.39096   0.0
> Si   9.74617   4.39096   0.0
> Si   2.17283   7.52804   0.0
> Si   9.74617   7.52804   0.0
> Si   2.17283  -0.0   7.52804
> Si   9.74617  -0.0   7.52804
> Si   2.17283  -0.0   4.39096
> Si   9.74617  -0.0   4.39096
> Si  -0.0   4.39096   9.74617
> Si  -0.0   4.39096   2.17283
> Si  -0.0   7.52804   9.74617
> Si  -0.0   7.52804   2.17283
> Si   4.39096   2.17283   0.0
> Si   4.39096   9.74617   0.0
> Si   7.52804   2.17283   0.0
> Si   7.52804   9.74617   0.0
> K_POINTS automatic
> 4 4 4 1 1 1
>
>
> PHONON INPUT
>
> normal modes for LTA
>  &inputph
>  tr2_ph=1.0d-14,
>  prefix='LTA',
>  epsil=.true.,
>  fildyn='LTA.dyn'
>  outdir='./scratch',
>  trans=.true.,
>  lraman=.true.,
> /
> 0.0 0.0 0.0
>
>
> Best regards,
>
> Amir M. Mofrad
>
>
> 
> From: pw_forum-boun...@pwscf.org  on behalf
> of Lorenzo Paulatto 
> Sent: Tuesday, February 2, 2016 2:46 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Phonon_Calculations
>
> On Monday, February 01, 2016 09:26:39 PM Mofrad, Amir Mehdi wrote:
> > Dear all QE devel

Re: [Pw_forum] coefficients of plane wave

2016-02-02 Thread Jia Chen

Dear Eliya Asmani,

I had the same problem one week ago, and found pw2casino particularly
helpful. Maybe you want to check it out.

Cheers
Jia

On Tue, Feb 2, 2016 at 3:13 PM, Eliya Asmani  wrote:

> Dear all
>
> I need to have the coefficients of plane wave, I mean evc.dat and
> gkvector.dat. But these files are binary. How can I convert them to ASCII
> format?
>
>
>
>
> Eliya Asmani,
> Postdoctoral Researcher
> School of Physics, Institute for Research in Fundamental Sciences (IPM)
> Tehran, Iran
>
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[Pw_forum] coefficients of plane wave

2016-02-02 Thread Eliya Asmani

Dear all

I need to have the coefficients of plane wave, I mean evc.dat and
gkvector.dat. But these files are binary. How can I convert them to ASCII
format?




Eliya Asmani,
Postdoctoral Researcher
School of Physics, Institute for Research in Fundamental Sciences (IPM)
Tehran, Iran
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Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread Goranka Bilalbegovic

>
>
> mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly
>
> However :
>
> mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It
> frozen in "Reading input from scf.in"
>
>
>
Hello Joaquin,

In the second raw you have pw,x  (with comma) not pw.x.  Of course, I do
not know if you did copy/paste from your script...

Best regards,

-- 
Goranka Bilalbegovic
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread joaquin peralta

Dear Paolo,

Setting the attr='' doesn't work, however comment out the call works like a
charm. So far it is probably a compiler/library/OS issue, because we tried
in a Debian 7.9 machine (with the same intel and intelmpi), and works
perfectly. The machine with the problem is a Debian testing.

Thanks in advance for all your help,
Joaquin

On Tue, Feb 2, 2016 at 2:15 PM Paolo Giannozzi 
wrote:

> Since you are not reading from xml, try to set attr=' ' before that call,
> or to comment out the call. The only reason I can think of (that doesn't
> imply a compiler/library/mpi weirdness) is that attr may not be set to
> anything if reading from a text file, and sometimes code get confused if a
> non-initialized variable is broadcast
>
> Paolo
>
> On Tue, Feb 2, 2016 at 6:07 PM, joaquin peralta 
> wrote:
>
>> Dear Paolo,
>>
>> Thank you very much for your promptly response. I found the line where
>> the code freezes.
>>
>> CALL mp_bcast( attr, ionode_id, intra_image_comm )
>>
>> However I can't figured out what could be the reason, or how to avoid the
>> hung.
>>
>> Do you have any additional suggestion?
>>
>> Thanks in advance,
>> Joaquin Peralta
>> Assitant Professor,
>> Faculty of Physics,
>> Exact Science Department,
>> Universidad Andres Bello,
>> Santaigo, Chile.
>>
>>
>> On Tue, Feb 2, 2016 at 1:23 PM Paolo Giannozzi 
>> wrote:
>>
>>> Go to Modules/read_input.f90, where routine "open_input_file" is called
>>> (should be line 50), and follow what happens later and where the code
>>> freezes. Just add some prints: there are smarter ways to figure out where a
>>> code is hung, but I don't remember how to do it. Once you find the exact
>>> line where it freezes, either you easily find why, or, if there is no
>>> obvious reason, it is likely a problem of your compiler/ libraries  / mpi.
>>>
>>> Paolo
>>>
>>>
>>> On Tue, Feb 2, 2016 at 4:40 PM, joaquin peralta 
>>> wrote:
>>>
 Dear Youssef,

 I did the compilation as you indicated, however my QE-run frozen with
 more than one CPU. I have the intel parallel studio 2016 and the impi 5.1.
 After compile I did :

 mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly

 However :

 mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It
 frozen in "Reading input from scf.in"

 Do you have any suggestion or hint about what could be the reason
 because is not working?

 I have all the exports from intel-suite in my bashrc :
 source /opt/intel/bin/compilervars.sh intel64
 source /opt/intel/mkl/bin/mklvars.sh intel64
 source /opt/intel/impi/5.1.2.150/bin64/mpivars.sh

 And I also set my stack size to unlimited in the kernel settings.

 Is there a code issue? Or is the intel mpi?

 Thanks in advance,
 Joaquin Peralta
 Assitant Professor,
 Faculty of Physics,
 Exact Science Department,
 Universidad Andres Bello,
 Santaigo, Chile.


 On Tue, Feb 2, 2016 at 9:57 AM Youssef  wrote:

> Dear
>
>
>
> *Yeonung, I used to compile qe-5.30 with intel parallel studio 2016,
> using this statements: *
>
>
>
>
>
>
>
>
>
>
>
>
> *export FC=mpiifort export F90=mpiifort export F77=mpiifort export
> MPIF90=mpiifort export CC=mpiicc export CPP="icc -E" export 
> CFLAGS=$FCFLAGS
> export AR=xiar export BLAS_LIBS="" export
> LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64" export
> SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" export
> FFT_LIBS="-L$MKLROOT/intel64" ./configure  --enable-parallel *
> you can save it as a bash script, an run it inside qe folder.
>
> Of course  make sure that the intel parallel studio wrapper is in your
> path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  
> invoke
> all the needed environmental variables.
>
> Youssef Aharbil,
>
> Laboratory of Physics and Chemistry of Materials
>
> Faculty of sciences Ben msik, Casablanca
>
> Morocco
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum


 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum

>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche In

Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread Paolo Giannozzi

Since you are not reading from xml, try to set attr=' ' before that call,
or to comment out the call. The only reason I can think of (that doesn't
imply a compiler/library/mpi weirdness) is that attr may not be set to
anything if reading from a text file, and sometimes code get confused if a
non-initialized variable is broadcast

Paolo

On Tue, Feb 2, 2016 at 6:07 PM, joaquin peralta  wrote:

> Dear Paolo,
>
> Thank you very much for your promptly response. I found the line where the
> code freezes.
>
> CALL mp_bcast( attr, ionode_id, intra_image_comm )
>
> However I can't figured out what could be the reason, or how to avoid the
> hung.
>
> Do you have any additional suggestion?
>
> Thanks in advance,
> Joaquin Peralta
> Assitant Professor,
> Faculty of Physics,
> Exact Science Department,
> Universidad Andres Bello,
> Santaigo, Chile.
>
>
> On Tue, Feb 2, 2016 at 1:23 PM Paolo Giannozzi 
> wrote:
>
>> Go to Modules/read_input.f90, where routine "open_input_file" is called
>> (should be line 50), and follow what happens later and where the code
>> freezes. Just add some prints: there are smarter ways to figure out where a
>> code is hung, but I don't remember how to do it. Once you find the exact
>> line where it freezes, either you easily find why, or, if there is no
>> obvious reason, it is likely a problem of your compiler/ libraries  / mpi.
>>
>> Paolo
>>
>>
>> On Tue, Feb 2, 2016 at 4:40 PM, joaquin peralta 
>> wrote:
>>
>>> Dear Youssef,
>>>
>>> I did the compilation as you indicated, however my QE-run frozen with
>>> more than one CPU. I have the intel parallel studio 2016 and the impi 5.1.
>>> After compile I did :
>>>
>>> mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly
>>>
>>> However :
>>>
>>> mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It
>>> frozen in "Reading input from scf.in"
>>>
>>> Do you have any suggestion or hint about what could be the reason
>>> because is not working?
>>>
>>> I have all the exports from intel-suite in my bashrc :
>>> source /opt/intel/bin/compilervars.sh intel64
>>> source /opt/intel/mkl/bin/mklvars.sh intel64
>>> source /opt/intel/impi/5.1.2.150/bin64/mpivars.sh
>>>
>>> And I also set my stack size to unlimited in the kernel settings.
>>>
>>> Is there a code issue? Or is the intel mpi?
>>>
>>> Thanks in advance,
>>> Joaquin Peralta
>>> Assitant Professor,
>>> Faculty of Physics,
>>> Exact Science Department,
>>> Universidad Andres Bello,
>>> Santaigo, Chile.
>>>
>>>
>>> On Tue, Feb 2, 2016 at 9:57 AM Youssef  wrote:
>>>
 Dear



 *Yeonung, I used to compile qe-5.30 with intel parallel studio 2016,
 using this statements: *












 *export FC=mpiifort export F90=mpiifort export F77=mpiifort export
 MPIF90=mpiifort export CC=mpiicc export CPP="icc -E" export CFLAGS=$FCFLAGS
 export AR=xiar export BLAS_LIBS="" export
 LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64" export
 SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" export
 FFT_LIBS="-L$MKLROOT/intel64" ./configure  --enable-parallel *
 you can save it as a bash script, an run it inside qe folder.

 Of course  make sure that the intel parallel studio wrapper is in your
 path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  invoke
 all the needed environmental variables.

 Youssef Aharbil,

 Laboratory of Physics and Chemistry of Materials

 Faculty of sciences Ben msik, Casablanca

 Morocco



 ___
 Pw_forum mailing list
 Pw_forum@pwscf.org
 http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> 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
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
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
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread joaquin peralta

Dear Paolo,

Thank you very much for your promptly response. I found the line where the
code freezes.

CALL mp_bcast( attr, ionode_id, intra_image_comm )

However I can't figured out what could be the reason, or how to avoid the
hung.

Do you have any additional suggestion?

Thanks in advance,
Joaquin Peralta
Assitant Professor,
Faculty of Physics,
Exact Science Department,
Universidad Andres Bello,
Santaigo, Chile.


On Tue, Feb 2, 2016 at 1:23 PM Paolo Giannozzi 
wrote:

> Go to Modules/read_input.f90, where routine "open_input_file" is called
> (should be line 50), and follow what happens later and where the code
> freezes. Just add some prints: there are smarter ways to figure out where a
> code is hung, but I don't remember how to do it. Once you find the exact
> line where it freezes, either you easily find why, or, if there is no
> obvious reason, it is likely a problem of your compiler/ libraries  / mpi.
>
> Paolo
>
>
> On Tue, Feb 2, 2016 at 4:40 PM, joaquin peralta 
> wrote:
>
>> Dear Youssef,
>>
>> I did the compilation as you indicated, however my QE-run frozen with
>> more than one CPU. I have the intel parallel studio 2016 and the impi 5.1.
>> After compile I did :
>>
>> mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly
>>
>> However :
>>
>> mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It
>> frozen in "Reading input from scf.in"
>>
>> Do you have any suggestion or hint about what could be the reason because
>> is not working?
>>
>> I have all the exports from intel-suite in my bashrc :
>> source /opt/intel/bin/compilervars.sh intel64
>> source /opt/intel/mkl/bin/mklvars.sh intel64
>> source /opt/intel/impi/5.1.2.150/bin64/mpivars.sh
>>
>> And I also set my stack size to unlimited in the kernel settings.
>>
>> Is there a code issue? Or is the intel mpi?
>>
>> Thanks in advance,
>> Joaquin Peralta
>> Assitant Professor,
>> Faculty of Physics,
>> Exact Science Department,
>> Universidad Andres Bello,
>> Santaigo, Chile.
>>
>>
>> On Tue, Feb 2, 2016 at 9:57 AM Youssef  wrote:
>>
>>> Dear
>>>
>>>
>>>
>>> *Yeonung, I used to compile qe-5.30 with intel parallel studio 2016,
>>> using this statements: *
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *export FC=mpiifort export F90=mpiifort export F77=mpiifort export
>>> MPIF90=mpiifort export CC=mpiicc export CPP="icc -E" export CFLAGS=$FCFLAGS
>>> export AR=xiar export BLAS_LIBS="" export
>>> LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64" export
>>> SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" export
>>> FFT_LIBS="-L$MKLROOT/intel64" ./configure  --enable-parallel *
>>> you can save it as a bash script, an run it inside qe folder.
>>>
>>> Of course  make sure that the intel parallel studio wrapper is in your
>>> path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  invoke
>>> all the needed environmental variables.
>>>
>>> Youssef Aharbil,
>>>
>>> Laboratory of Physics and Chemistry of Materials
>>>
>>> Faculty of sciences Ben msik, Casablanca
>>>
>>> Morocco
>>>
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> 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
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
___
Pw_forum mailing list
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Re: [Pw_forum] Phonon_Calculations

2016-02-02 Thread Mofrad, Amir Mehdi (MU-Student)

Thank you for your reply Dr. Paulatto. The problem is that I used to run the 
same type of calculation (scf first and then phonon calculation) on my personal 
computers and never had got this error (I got other errors which I was able to 
solve). However, when I try to do this calculation on a cluster it gives me the 
error that I mentioned in the previous email. In order to be clear, I put the 
input files of both scf and phonon calculations here:

SCF INPUT: 

&CONTROL
 calculation = 'scf' ,
restart_mode = 'from_scratch' ,
  wf_collect = .true. ,
  outdir = './scratch' ,
  wfcdir = './scratch' ,
  pseudo_dir = '../../../pseudo' ,
  prefix = 'LTA' ,
   verbosity = 'high' ,
   etot_conv_thr = 1e-5 ,
   forc_conv_thr = 1e-4 ,
   nstep = 50 ,
 tstress = .true. ,
 tprnfor = .true. ,
 /

 &SYSTEM
   ibrav = 0,
 nat =72 ,
ntyp = 2,
 ecutwfc = 90 ,
 ecutrho = 360 ,
 /

 &ELECTRONS
electron_maxstep = 100,
conv_thr = 3e-8 ,
 mixing_mode = 'plain' ,
 mixing_beta = 0.7 ,
 diagonalization = 'david' ,
/


CELL_PARAMETERS angstrom

  11.91900   0.0   0.0
  0.0  11.91900   0.0
  0.0   0.0  11.91900
ATOMIC_SPECIES
Si   28.08600  Si.pz-hgh.UPF
O   15.99940  O.pz-hgh.UPF

ATOMIC_POSITIONS angstrom
 O  -0.0   2.52921   5.95950
 O   1.31467   1.31467   4.03339
 O  -0.0   3.53637   3.53637
Si  -0.0   2.17283   4.39096
 O  -0.0   9.38979   5.95950
 O   5.95950  -0.0   2.52921
 O   5.95950  -0.0   9.38979
 O   2.52921   5.95950   0.0
 O   9.38979   5.95950   0.0
 O   2.52921  -0.0   5.95950
 O   9.38979  -0.0   5.95950
 O  -0.0   5.95950   9.38979
 O  -0.0   5.95950   2.52921
 O   5.95950   2.52921   0.0
 O   5.95950   9.38979   0.0
 O  10.60433  10.60433   4.03339
 O  10.60433   1.31467   7.88561
 O   1.31466  10.60433   7.88561
 O   4.03339   1.31467   1.31467
 O   4.03339  10.60433  10.60433
 O   7.88561  10.60433   1.31467
 O   7.88561   1.31467  10.60433
 O   1.31467   4.03339   1.31467
 O  10.60433   4.03339  10.60433
 O   1.31466   7.88561  10.60433
 O  10.60433   7.88561   1.31467
 O   1.31467   1.31467   7.88561
 O  10.60433  10.60433   7.88561
 O   1.31466  10.60433   4.03339
 O  10.60433   1.31467   4.03339
 O   1.31467   4.03339  10.60433
 O  10.60433   4.03339   1.31467
 O  10.60433   7.88561  10.60433
 O   1.31467   7.88561   1.31467
 O   4.03339   1.31467  10.60433
 O   4.03339  10.60433   1.31467
 O   7.88561   1.31467   1.31467
 O   7.88561  10.60433  10.60433
 O  -0.0   8.38263   3.53637
 O  -0.0   3.53637   8.38263
 O  -0.0   8.38263   8.38263
 O   3.53637  -0.0   3.53637
 O   3.53637  -0.0   8.38263
 O   8.38263  -0.0   3.53637
 O   8.38263  -0.0   8.38263
 O   3.53637   3.53637   0.0
 O   8.38263   3.53637   0.0
 O   3.53637   8.38263   0.0
 O   8.38263   8.38263   0.0
Si  -0.0   9.74617   4.39096
Si  -0.0   2.17283   7.52804
Si  -0.0   9.74617   7.52804
Si   4.39096  -0.0   2.17283
Si   4.39096  -0.0   9.74617
Si   7.52804  -0.0   2.17283
Si   7.52804  -0.0   9.74617
Si   2.17283   4.39096   0.0
Si   9.74617   4.39096   0.0
Si   2.17283   7.52804   0.0
Si   9.74617   7.52804   0.0
Si   2.17283  -0.0   7.52804
Si   9.74617  -0.0   7.52804
Si   2.17283  -0.0   4.39096
Si   9.74617  -0.0   4.39096
Si  -0.0   4.39096   9.74617
Si  -0.0   4.39096   2.17283
Si  -0.0   7.52804   9.74617
Si  -0.0   7.52804   2.17283
Si   4.39096   2.17283   0.0
Si   4.39096   9.74617   0.0
Si   7.52804   2.17283   0.0
Si   7.52804   9.74617   0.0
K_POINTS automatic
4 4 4 1 1 1
 

PHONON INPUT 

normal modes for LTA
 &inputph
 tr2_ph=1.0d-14,
 prefix='LTA',
 epsil=.true.,
 fildyn='LTA.dyn'
 outdir='./scratch',
 trans=.true.,
 lraman=.true.,
/
0.0 0.0 0.0


Best regards, 

Amir M. Mofrad



From: pw_forum-boun...@pwscf.org  on behalf of 
Lorenzo Paulatto 
Sent: Tuesday, February 2, 2016 2:46 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Phonon_Calculations

On Monday, February 01, 2016 09:26:39 PM Mofrad, Amir Mehdi wrote:
> Dear all QE developers and experts,
>
> I am trying to do a phonon calculations but I get the following error which
> I can't solve:
>

Dear Amir,
this error means tha tthe phonon code cannon find the wavefuntions from the
non-self consisten calculation which is performed at the beginning of the run.
there are many possible causes for it, you will need to provide more details
(i.e. input files, running environment) to have a proper

Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread Paolo Giannozzi

Go to Modules/read_input.f90, where routine "open_input_file" is called
(should be line 50), and follow what happens later and where the code
freezes. Just add some prints: there are smarter ways to figure out where a
code is hung, but I don't remember how to do it. Once you find the exact
line where it freezes, either you easily find why, or, if there is no
obvious reason, it is likely a problem of your compiler/ libraries  / mpi.

Paolo


On Tue, Feb 2, 2016 at 4:40 PM, joaquin peralta  wrote:

> Dear Youssef,
>
> I did the compilation as you indicated, however my QE-run frozen with more
> than one CPU. I have the intel parallel studio 2016 and the impi 5.1. After
> compile I did :
>
> mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly
>
> However :
>
> mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It
> frozen in "Reading input from scf.in"
>
> Do you have any suggestion or hint about what could be the reason because
> is not working?
>
> I have all the exports from intel-suite in my bashrc :
> source /opt/intel/bin/compilervars.sh intel64
> source /opt/intel/mkl/bin/mklvars.sh intel64
> source /opt/intel/impi/5.1.2.150/bin64/mpivars.sh
>
> And I also set my stack size to unlimited in the kernel settings.
>
> Is there a code issue? Or is the intel mpi?
>
> Thanks in advance,
> Joaquin Peralta
> Assitant Professor,
> Faculty of Physics,
> Exact Science Department,
> Universidad Andres Bello,
> Santaigo, Chile.
>
>
> On Tue, Feb 2, 2016 at 9:57 AM Youssef  wrote:
>
>> Dear
>>
>>
>>
>> *Yeonung, I used to compile qe-5.30 with intel parallel studio 2016,
>> using this statements: *
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *export FC=mpiifort export F90=mpiifort export F77=mpiifort export
>> MPIF90=mpiifort export CC=mpiicc export CPP="icc -E" export CFLAGS=$FCFLAGS
>> export AR=xiar export BLAS_LIBS="" export
>> LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64" export
>> SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" export
>> FFT_LIBS="-L$MKLROOT/intel64" ./configure  --enable-parallel *
>> you can save it as a bash script, an run it inside qe folder.
>>
>> Of course  make sure that the intel parallel studio wrapper is in your
>> path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  invoke
>> all the needed environmental variables.
>>
>> Youssef Aharbil,
>>
>> Laboratory of Physics and Chemistry of Materials
>>
>> Faculty of sciences Ben msik, Casablanca
>>
>> Morocco
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
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
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

Re: [Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread joaquin peralta

Dear Youssef,

I did the compilation as you indicated, however my QE-run frozen with more
than one CPU. I have the intel parallel studio 2016 and the impi 5.1. After
compile I did :

mpirun -np 1 /path/to/pw.x -input scf.in <-This run perfectly

However :

mpirun -np 2 /path/to/pw,x -input scf.in  <- Doesn't work!!!, It frozen
in "Reading input from scf.in"

Do you have any suggestion or hint about what could be the reason because
is not working?

I have all the exports from intel-suite in my bashrc :
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/mkl/bin/mklvars.sh intel64
source /opt/intel/impi/5.1.2.150/bin64/mpivars.sh

And I also set my stack size to unlimited in the kernel settings.

Is there a code issue? Or is the intel mpi?

Thanks in advance,
Joaquin Peralta
Assitant Professor,
Faculty of Physics,
Exact Science Department,
Universidad Andres Bello,
Santaigo, Chile.


On Tue, Feb 2, 2016 at 9:57 AM Youssef  wrote:

> Dear
>
>
>
> *Yeonung, I used to compile qe-5.30 with intel parallel studio 2016, using
> this statements: *
>
>
>
>
>
>
>
>
>
>
>
>
> *export FC=mpiifort export F90=mpiifort export F77=mpiifort export
> MPIF90=mpiifort export CC=mpiicc export CPP="icc -E" export CFLAGS=$FCFLAGS
> export AR=xiar export BLAS_LIBS="" export
> LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64" export
> SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" export
> FFT_LIBS="-L$MKLROOT/intel64" ./configure  --enable-parallel *
> you can save it as a bash script, an run it inside qe folder.
>
> Of course  make sure that the intel parallel studio wrapper is in your
> path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  invoke
> all the needed environmental variables.
>
> Youssef Aharbil,
>
> Laboratory of Physics and Chemistry of Materials
>
> Faculty of sciences Ben msik, Casablanca
>
> Morocco
>
>
>
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[Pw_forum] Virtual NanoLab - A Free GUI for Quantum Espresso.

2016-02-02 Thread Daniele Stradi


Dear Quantum Espresso users,

QuantumWise (/www.quantumwise.com/) is happy to announce the*Virtual NanoLab 
(VNL) FREE graphical user interface for Quantum Espresso*!

*- VNL features (see more at /http://quantumwise.com/products/vnl/)*

VNL offers a wide range of tools for building atomic geometry for molecules, 
crystals, surfaces, nanostructures,
and devices. These include*3D manipulation tools*, a*surface cleaver*, 
an*interface builder*, and a*molecular builder*.

VNL is available for*Linux*,*Windows*, and*Mac OS*  through self-contained 
binary installers – no compilation
needed, and no external library dependencies beyond standard OS packages.

*VNL is FREE*  if you work as an*academic researcher*  at a university, 
college, or similar – just*fill out the form at this link to obtain a FREE 
perpetual license*:/http://www.quantumwise.com/free-trial/free-vnl/

Researchers and engineers working in industrial companies and government labs 
can purchase licenses for VNL
by contacting us at this link:/http://www.quantumwise.com/about-us/contact-us/

*- VNL is tightly integrated with Quantum Espresso*

The import/export capabilities of VNL allow you to*export structures directly 
to a Quantum Espresso input*.
Quantities such as*density grids*,*band structures*, and*density of states*  
can be analyzed in VNL by directly*importing them from the output of a Quantum 
Espresso calculation*. We invite you to check our dedicated
tutorials:

- VNL as a GUI for Quantum Espresso:
/http://docs.quantumwise.com/tutorials/espresso_gui.html/

- Silicon bandstructure and DOS using VNL and Quantum Espresso:
/http://docs.quantumwise.com/tutorials/espresso_bs_dos.html/

A*full-featured scripter for Quantum Espresso*  is on its way and will be 
released soon, allowing you to set up
your Quantum Espresso calculations directly from within VNL! You can also 
tailor VNL to your specific research
needs by*writing your own Plug-in*  (see more 
at/http://docs.quantumwise.com/tutorials/addons.html/).

We hope you will enjoy VNL as much as our current users do! Have a look at the 
testimonials
and see what they say about the 
software:/http://quantumwise.com/products/testimonials/

Sincerely,

The QuantumWise team

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Re: [Pw_forum] Dielectric Constant Using Phonon

2016-02-02 Thread Marton

Hi Kanak,

Does your system contain three layers of MoS2 and some vacuum along z? If
yes, then the high frequency dielectric constant will approach 1 as you
increase the size of the vacuum or in other words the interlayer separation.

There is a nice discussion why this should happen for example in

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.88.245309

In particular, check Fig.7. and the related section.

Sincerely,
Marton Voros

--
Aneesur Rahman Fellow
Materials Science Division
Argonne National Laboratory

On Tue, Feb 2, 2016 at 3:45 AM, Kanak Datta  wrote:

> Dear researchers
>
> I have been trying to calculate the dielectric constant of multilayer TMDC
> materials. I have used the ph.x package of quantum espresso for this. From
> simulation I have got the following values:
>
>   Dielectric constant in cartesian axis
>
>   (   6.990898310   0.0   0.0 )
>   (   0.0   6.990898310   0.0 )
>   (   0.0   0.0   1.52669 )
>
> The values were obtained for Mos2 trilayer. I did the scf calculation
> before using the phonon package. The following code was used for phonon:
>
> &inputph
>   tr2_ph=1.0d-14,
>   prefix='MoS2AAA187',
>   epsil=.true.
>   outdir='D:\Quantum ESPRESSO 64-bit 5.1.2-mpich2\MoS2AAA187\outdir',
>   !outdir='./'
>   fildyn='MoS2AAA187.dynG',
>
>  /
>  0.0 0.0 0.0
>
> For scf calculation I used pbe-hgh pseudopotentials.
> The question is, why the z axis value of dielectric constant is so low?
> Values found in the literature is typically close. Is there something that
> must be added in phonon package?
>
> Thanks in advance.
>
> Sincerely yours
> Kanak
> EEE, BUET
>
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[Pw_forum] Compilation with intel compiler and MKL.

2016-02-02 Thread Youssef


Dear *Yeonung,

I used to compile qe-5.30 with intel parallel studio 2016, using this 
statements:


**export FC=mpiifort
export F90=mpiifort
export F77=mpiifort
export MPIF90=mpiifort
export CC=mpiicc
export CPP="icc -E"
export CFLAGS=$FCFLAGS
export AR=xiar
export BLAS_LIBS=""
export LAPACK_LIBS="-lmkl_blacs_intelmpi_lp64"
export SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64"
export FFT_LIBS="-L$MKLROOT/intel64"
./configure  --enable-parallel
*
you can save it as a bash script, an run it inside qe folder.

Of course  make sure that the intel parallel studio wrapper is in your 
path (e.g. :  source /opt/intel/bin/compilervars.sh intel64 ), this  
invoke all the needed environmental variables.


Youssef Aharbil,

Laboratory of Physics and Chemistry of Materials

Faculty of sciences Ben msik, Casablanca

Morocco



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[Pw_forum] PWgui installation Problem

2016-02-02 Thread Youssef



Dear Muthu.V ,
Have tried :
sudo apt-get install tcl8.5 iwidgets4

Youssef Aharbil,
Laboratory of Physics and Chemistry of Materials
Faculty of sciences Ben msik, Casablanca
Morocco

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[Pw_forum] So many atomic wfc

2016-02-02 Thread Hüseyin Yasin Uzunok

Dear QE developers,

While i tried to calculate partial dos with spin-orbit interaction i had
received an error message as follows;

 %%
 task # 0
 from partialdos_nc : error #31
 file extension not supporting so many atomic wfc
 %%

I guess that the problem is upcoming from the number of allowed wfc but i
could not find any way to increase it. I would appreciate any help that you
can suggest.
Yours.

P.S. the partial dos input is  as following;


cat > pdos.in <___
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[Pw_forum] Quantum-ESPRESSO School on Ab-Initio Thermal Transport

2016-02-02 Thread Lorenzo Paulatto

Dear Quantum-ESPRESSO users, I hope this announcement will be interesting for 
you. Lorenzo

Quantum-ESPRESSO School on Ab-Initio Thermal Transport

*27-30 June 2016 - Université Pierre et Marie Curie - Paris 6 (France)*

Organizers: Lorenzo Paulatto (IMPMC, Université Paris 6/CNRS, FR) Giorgia
Fugallo (ETSF/LSI, Ecole Polytechnique, Palaiseau, FR), Andrea Cepellotti
(EPFL, CH) and Francesco Mauri (Università di Roma La Sapienza, IT).

This school will provide the conceptual and computational tools to predict
the intrinsic phonon-driven thermal transport of materials, fully
ab-initio. The school will be composed of two parts: (1) introduction to
density functional theory, total energy calculations and phonons, and (2)
anharmonicity and thermal transport, by means of the generalized density
functional perturbation theory and the Boltzmann transport equation.

Confirmed speakers:

Nicola Bonini, King’s College London, UK

Andrea Cepellotti, École Polytechnique Fédérale, Lausanne, Switzerland

Giorgia Fugallo, École Polytechnique, Palaiseau, France

Francesco Mauri, Università di Roma La Sapienza, Rome, Italy

Lorenzo Paulatto, IMPMC/CNRS, Paris, France

Guilherme Ribeiro, IMPMC/UPMC, Paris France

Invited speakers to be confirmed:

Stefano de Gironcoli, SISSA, Trieste, Italy

Christian Carbogno, Fritz Haber Institut, Berlin, Germany


To register or to request any additional information please write to
. A limited number of travel and lodge allowances is
available, if you wish to apply for one please join to your registration
request a curriculum vitae and a short motivation letter and a
recommendation letter from your supervisor. For more information a updates you 
can refer to the school website .

Ab-initio prediction of thermal properties for condensed matter has been a
blossoming field in the last few years, thank to its numerous applications
mainly in thermoelectric materials and heat dissipation technologies. This
methodology however does require to master a certain amount of expertise,
both technical and theoretical, in order to be executed rigorously and
efficiently. In this school, we want to provide an in-depth view of the
theoretical framework, without neglecting the importance of applying the
theory on some practical examples. The school will be composed of theory
sessions and hands-on tutorials suitable for anybody with graduate-level
knowledge of condensed matter physics. This school will also serve as a
launch event for the public release of open-source codes for thermal
transport.

In the first part of the school we take every participant to a
working-level knowledge of density functional theory. We want to treat the
basic theory and the most common technical challenges of a plane-wave
calculation, such as construction and optimization of simulation cells,
choice of functional and pseudopotentials, convergence with basis set
cutoff and k-points sampling. This introductory part should be covered in
two days, comprising of lectures in the morning and hands-on sessions in
the afternoon.

The core focus of the school will be on the advanced topics of the
following two days. We will start from the harmonic model: ions are assumed
to vibrate within a small radius around their equilibrium positions, under
the effect of forces which can be accurately described as a superposition
of 2-body harmonic potentials. Lattice vibrations can be decomposed as a
set of monochromatic waves, called phonons, that can be easily
characterized using plane waves calculations. Phonons of wavevector q can
be obtained as eigenvectors of the dynamical matrix, i.e. the second
derivative of the total energy with respect to a periodic atom displacement
of periodicity dual to q.

Nevertheless, several interesting phenomena cannot be accounted in a purely
harmonic model because of one key limitation: the phonons are stationary
states of the harmonic hamiltonian that do not interact with each other in
a harmonic crystal. Furthermore, they are bosonic quasiparticles, hence
there is no limit to the amount of heat that can be carried by a phonon. In
other words, the thermal conductivity of a perfect harmonic crystal is
always infinite. In order to have a realistic description, anharmonicity
has to be taken into account.

If the system is not close to melting point, anharmonicity can be treated
perturbatively. The lowest term in perturbation theory requires the
calculation of three-body force constants, i.e. the derivative of the total
energy with respect to three harmonic perturbations. These derivatives can
be computed from first principles using the “2n+1” theorem, which allows
the calculation of both 2nd and 3rd order derivatives just by the knowledge
of the first order wave function response. The phonon lifetime can be
straightforwardly derived from their interaction and plugged into the
phonon Boltzmann transport equation. Solving the Boltzmann equation is a
difficult problem

[Pw_forum] Dielectric Constant Using Phonon

2016-02-02 Thread Kanak Datta

Dear researchers

I have been trying to calculate the dielectric constant of multilayer TMDC
materials. I have used the ph.x package of quantum espresso for this. From
simulation I have got the following values:

  Dielectric constant in cartesian axis

  (   6.990898310   0.0   0.0 )
  (   0.0   6.990898310   0.0 )
  (   0.0   0.0   1.52669 )

The values were obtained for Mos2 trilayer. I did the scf calculation
before using the phonon package. The following code was used for phonon:

&inputph
  tr2_ph=1.0d-14,
  prefix='MoS2AAA187',
  epsil=.true.
  outdir='D:\Quantum ESPRESSO 64-bit 5.1.2-mpich2\MoS2AAA187\outdir',
  !outdir='./'
  fildyn='MoS2AAA187.dynG',

 /
 0.0 0.0 0.0

For scf calculation I used pbe-hgh pseudopotentials.
The question is, why the z axis value of dielectric constant is so low?
Values found in the literature is typically close. Is there something that
must be added in phonon package?

Thanks in advance.

Sincerely yours
Kanak
EEE, BUET
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Re: [Pw_forum] Phonon_Calculations

2016-02-02 Thread Lorenzo Paulatto

On Monday, February 01, 2016 09:26:39 PM Mofrad, Amir Mehdi wrote:
> Dear all QE developers and experts,
> 
> I am trying to do a phonon calculations but I get the following error which
> I can't solve:
> 

Dear Amir,
this error means tha tthe phonon code cannon find the wavefuntions from the 
non-self consisten calculation which is performed at the beginning of the run. 
there are many possible causes for it, you will need to provide more details 
(i.e. input files, running environment) to have a proper answer.

kind regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/
23-24/4é16 Boîte courrier 115, 
4 place Jussieu 75252 Paris Cédex 05

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Re: [Pw_forum] coefficients of plane wave

Re: [Pw_forum] coefficients of plane wave

Re: [Pw_forum] coefficients of plane wave

Re: [Pw_forum] coefficients of plane wave

Re: [Pw_forum] So many atomic wfc

Re: [Pw_forum] Phonon_Calculations

Re: [Pw_forum] So many atomic wfc

Re: [Pw_forum] Phonon_Calculations

Re: [Pw_forum] coefficients of plane wave

[Pw_forum] coefficients of plane wave

Re: [Pw_forum] Compilation with intel compiler and MKL.

Re: [Pw_forum] Compilation with intel compiler and MKL.

Re: [Pw_forum] Compilation with intel compiler and MKL.

Re: [Pw_forum] Compilation with intel compiler and MKL.

Re: [Pw_forum] Phonon_Calculations

Re: [Pw_forum] Compilation with intel compiler and MKL.

Re: [Pw_forum] Compilation with intel compiler and MKL.

[Pw_forum] Virtual NanoLab - A Free GUI for Quantum Espresso.

Re: [Pw_forum] Dielectric Constant Using Phonon

[Pw_forum] Compilation with intel compiler and MKL.

[Pw_forum] PWgui installation Problem

[Pw_forum] So many atomic wfc

[Pw_forum] Quantum-ESPRESSO School on Ab-Initio Thermal Transport

[Pw_forum] Dielectric Constant Using Phonon

Re: [Pw_forum] Phonon_Calculations

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