[Pw_forum] Pw_forum Digest, Vol 107, Issue 9

Leo freephys at gmail.com
Thu Jun 9 13:09:33 CEST 2016


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On June 9, 2016 6:00:01 AM EDT, pw_forum-request at pwscf.org wrote:
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>Today's Topics:
>
>   1. pseudo potential generation problem (pranay biswas)
>   2. Re: inconsistent number of sticks (Paolo Giannozzi)
>   3. Re: monoclinic system number of atom generated is	incorrect
>      (Paolo Giannozzi)
>   4. Re: monoclinic system number of atom generated is	incorrect
>      (Lorenzo Don?)
>   5. Regarding ph.x (Manu Hegde)
>   6. Re: Regarding ph.x (Bahad?r SALMANKURT)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 8 Jun 2016 16:28:51 +0530
>From: pranay biswas <pranayinform at gmail.com>
>Subject: [Pw_forum] pseudo potential generation problem
>To: pw_forum at pwscf.org
>Message-ID:
>	<CADoT4gDqLf9bZr1R4r8_w5bhi-+YFNoSOGdVWO1eyD4DWymA6g at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Users/sir
>Is there any dependence of pseudo potential on 'file-pseudopw name' i
>mean
>above the file name put for pp file?
>
>-- 
>*Pranay Biswas*
>*email- pranayinform at gmail.com <pranayinform at gmail.com>*
>*mob- +918116780033*
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>------------------------------
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>Message: 2
>Date: Wed, 8 Jun 2016 19:49:57 +0200
>From: Paolo Giannozzi <p.giannozzi at gmail.com>
>Subject: Re: [Pw_forum] inconsistent number of sticks
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>	<CAPMgbCt8=uVoR+80cYXPHTUuXNjQetzfD75Q3Ks_DwGKGJPfuw at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>It works for me on 16 processors:
>
>     Parallelization info
>     --------------------
>   sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
>   Min         240     169     46                45775    27239    3856
>   Max         242     170     47                45784    27274    3869
>   Sum        3853    2713    745               732455   436189   61805
>
>   Dense  grid:   732455 G-vectors     FFT dimensions: (  75,  75, 288)
>   Smooth grid:   436189 G-vectors     FFT dimensions: (  64,  64, 243)
>
>Paolo
>
>On Tue, Jun 7, 2016 at 5:01 PM, ???? ????? <vaibhav.kaware at gmail.com>
>wrote:
>> Dear all,
>>
>> I am trying to calculate all electron charge densities for Bader
>charge
>> calculation.
>> Since QE 5.1.1 (which I was using till now) does not have the all
>electron
>> charge density
>> option in it pp.x, I have switched to the latest version QE 5.4.0.
>>
>> I could compile 5.4.0 without any errors using the ./configure , make
>all
>> routine.
>>
>> However, when I try to run the new compilation, it throws error:
>> (Input file cuvac.2.scf.in is attached with the mail)
>>
>>
>-----------------------------------------------------------------------------------------------------------------------------------------------------------
>> [vaibhav at dhrupad test]$ /opt/intel/mpi-rt/4.1.0/intel64/bin/mpiexec
>-np 16
>> /home/vaibhav/opt/QE/5.4.0/espresso-5.4.0/bin/pw.x -inp
>cuvac.2.scf.in
>>
>>
>>      Program PWSCF v.5.4.0 starts on  7Jun2016 at 19:16:45
>>
>>      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);
>>           URL http://www.quantum-espresso.org",
>>      in publications or presentations arising from this work. More
>details
>> at
>>      http://www.quantum-espresso.org/quote
>>
>>      Parallel version (MPI), running on    16 processors
>>      R & G space division:  proc/nbgrp/npool/nimage =      16
>>      Reading input from cuvac.2.scf.in
>> Warning: card &IONS ignored
>> Warning: card / ignored
>> Warning: card &CELL ignored
>> Warning: card / ignored
>>
>>      Current dimensions of program PWSCF are:
>>      Max number of different atomic species (ntypx) = 10
>>      Max number of k-points (npk) =  40000
>>      Max angular momentum in pseudopotentials (lmaxx) =  3
>>      Presently no symmetry can be used with electric field
>>
>>
>>      IMPORTANT: XC functional enforced from input :
>>      Exchange-correlation      = VDW-DF ( 1  4  4  0 1 0)
>>      Any further DFT definition will be discarded
>>      Please, verify this is what you really want
>>
>>                file O.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s)  2P
>> renormalized
>>                file H.pbe-kjpaw_psl.0.1.UPF: wavefunction(s)  1S
>> renormalized
>>
>>      Subspace diagonalization in iterative solution of the eigenvalue
>> problem:
>>      one sub-group per band group will be used
>>      scalapack distributed-memory algorithm (size of sub-group:  2* 
>2
>> procs)
>>
>>   *                      1  *                      4  /=
>> 4
>>   *                      2  *                      4  /=
>> 4
>>
>> application called MPI_Abort(MPI_COMM_WORLD, 7) - process 12
>> application called MPI_Abort(MPI_COMM_WORLD, 7) - process 11
>> application called MPI_Abort(MPI_COMM_WORLD, 7) - process 8
>>
>>
>>
>>
>>
>>
>>
>>
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>      Error in routine  fft_dlay_set (7):
>>       inconsistent number of sticks
>>
>>
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>>      stopping ...
>>
>-----------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> I run this same example with 5.1.1, and it runs smooth. (Rather, I
>chose the
>> one that ran smooth with
>> 5.1.1).
>>
>> Is it a mesh related problem?
>> http://www.democritos.it/pipermail/pw_forum/2005-January/001876.html
>>
>> I wonder why it works fine in 5.1.1 but not in 5.4.0.
>>
>> I tried increasing the mesh values as nr1 = 144 , nr2 = 144 , nr3 =
>288
>> in accordance with:
>> http://www.democritos.it/pipermail/pw_forum/2011-April/020055.html
>>
>> but it did not help.
>>
>> Any and all help would be greatly appreciated.
>>
>> Thank you.
>>
>> --
>>
>> Vaibhav V. Kaware
>> c/o Dr. Kavita Joshi
>> CSIR-National Chemical Laboratory
>> Dr. Homi Bhabha Road
>> Pune 411 008
>> India
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at 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
>
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 8 Jun 2016 20:06:42 +0200
>From: Paolo Giannozzi <p.giannozzi at gmail.com>
>Subject: Re: [Pw_forum] monoclinic system number of atom generated is
>	incorrect
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>	<CAPMgbCvc3z++k78a=rXRvz-1ZvR1Ac8JvsUp3JN6Jhbtkd4GLQ at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>You should first of all figure out if your data is for "unique axis b"
>or "unique axis c". I think it is for the former case, so you should
>specifiy "uniqueb=.true.". See also the input documentation of pw.x.
>You also need to know the Wyckoff sites for your crystal:
>   http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list
>
>Paolo
>
>On Wed, Jun 8, 2016 at 11:17 AM, Lorenzo Don?
><lorechimica91 at hotmail.it> wrote:
>> Good morning to everyone
>> I am performing this calculation on a monoclinic system: Symmetry
>> information:
>> Monoclinic crystal system.
>> Space group number     : 15
>> Hall symbol            : -I 2ya
>> Hermann-Mauguin symbol : I12/a1
>> Symmetry equivalent sites:
>>    1         x,        y,        z
>>    2        -x,       -y,       -z
>>    3    -x+1/2,        y,       -z
>>    4     x+1/2,       -y,        z
>>
>> Lattice parameters:
>>           a           b           c
>>  23.8688000  11.1968000   7.8252000
>>       alpha        beta       gamma
>>  90.0000000  95.4750000  90.0000000
>> Bravais lattice vectors :
>>   1.0000000   0.0000000   0.0000000
>>   0.0000000   0.4690977   0.0000000
>>   0.4843601   0.2345489   0.1631733
>>  in which the number of atom is 72 but in my pw.x output I found 80
>atoms.
>> this is my input:
>>
>> &control
>>
>>     calculation='relax'
>>
>>     pseudo_dir='/Users/lorenzodona/Downloads/espresso-5.4.0/pseudo/'
>>
>>     verbosity= high,
>>
>> /
>>
>>  &system
>>
>>     a= 23.8688, b= 11.1968, c= 7.8252, cosab= 0.417083157,
>space_group = 15,
>>
>>     nat=  20, ntyp= 4,
>>
>>     ecutwfc =15.0,
>>
>>     rhombohedral= .false.
>>
>> /
>>
>>  &electrons
>>
>>     diagonalization='david'
>>
>>     mixing_beta = 0.7
>>
>>     conv_thr= 1.0e-7
>>
>> /
>>
>>  &ions
>>
>>  ion_dynamics='bfgs'
>>
>>  /
>>
>> ATOMIC_SPECIES
>>
>> Zr 91.224 Zr.pbe-mt_fhi.UPF
>>
>> C 12.010 C.pbe-mt_fhi.UPF
>>
>> O 16.00  O.pbe-mt_fhi.UPF
>>
>> H 1.00   H.pbe-mt_fhi.UPF
>>
>> ATOMIC_POSITIONS crystal_sg
>>
>> Zr      0.8055700   0.2260400   0.1404400
>>
>> O       0.7837400   0.2764700   0.3778600
>>
>> O       0.7887800   0.0352700   0.0965300
>>
>> O       0.8863700   0.2930100   0.0648300
>>
>> O       0.7894200   0.4193200   0.0923400
>>
>> O       0.8721000   0.1295600  -0.7030000
>>
>> C       0.8994700   0.1401400   0.4427600
>>
>> C       0.9514400   0.0679000   0.4731700
>>
>> C       0.9682300  -0.0035900   0.3401200
>>
>> C       0.0168300  -0.0717400   0.3668600
>>
>> C      -0.2965000  -0.2104000  -0.0790000
>>
>> C      -0.7034500  -0.6656900   0.0788000
>>
>> H       0.9426100  -0.0042000   0.2174500
>>
>> H       0.0307000   0.8716500   0.2661000
>>
>> H       0.3320300   0.3845300   0.1396500
>>
>> H       0.6681300   0.8400300   0.8596200
>>
>> C       0.7500000   0.4711800   0.0000000
>>
>> C       0.7500000   0.9838200   0.0000000
>>
>> C       0.7500000   0.8516100   0.0000000
>>
>> C       0.7500000   0.6036500   0.0000000
>>
>>
>> Can you tell me where I am making a mistake??
>> thanks a lot
>> dearly
>> lorenzo
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at 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
>
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 8 Jun 2016 21:08:15 +0200
>From: Lorenzo Don? <lorechimica91 at hotmail.it>
>Subject: Re: [Pw_forum] monoclinic system number of atom generated is
>	incorrect
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID: <BLU436-SMTP11679CE6E881C1E6666312FCB5E0 at phx.gbl>
>Content-Type: text/plain; charset="utf-8"
>
>Dear Paolo
>Thanks now it works
>Sorry but i have another question:
>where or how can i find the Bravais lattice vectors for a system??
>Is there some tools or web site??
>Thanks a lot again.
>> Il giorno 08 giu 2016, alle ore 20:06, Paolo Giannozzi
><p.giannozzi at gmail.com> ha scritto:
>> 
>> You should first of all figure out if your data is for "unique axis
>b"
>> or "unique axis c". I think it is for the former case, so you should
>> specifiy "uniqueb=.true.". See also the input documentation of pw.x.
>> You also need to know the Wyckoff sites for your crystal:
>>   http://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list
>> 
>> Paolo
>> 
>> On Wed, Jun 8, 2016 at 11:17 AM, Lorenzo Don?
><lorechimica91 at hotmail.it> wrote:
>>> Good morning to everyone
>>> I am performing this calculation on a monoclinic system: Symmetry
>>> information:
>>> Monoclinic crystal system.
>>> Space group number     : 15
>>> Hall symbol            : -I 2ya
>>> Hermann-Mauguin symbol : I12/a1
>>> Symmetry equivalent sites:
>>>   1         x,        y,        z
>>>   2        -x,       -y,       -z
>>>   3    -x+1/2,        y,       -z
>>>   4     x+1/2,       -y,        z
>>> 
>>> Lattice parameters:
>>>          a           b           c
>>> 23.8688000  11.1968000   7.8252000
>>>      alpha        beta       gamma
>>> 90.0000000  95.4750000  90.0000000
>>> Bravais lattice vectors :
>>>  1.0000000   0.0000000   0.0000000
>>>  0.0000000   0.4690977   0.0000000
>>>  0.4843601   0.2345489   0.1631733
>>> in which the number of atom is 72 but in my pw.x output I found 80
>atoms.
>>> this is my input:
>>> 
>>> &control
>>> 
>>>    calculation='relax'
>>> 
>>>    pseudo_dir='/Users/lorenzodona/Downloads/espresso-5.4.0/pseudo/'
>>> 
>>>    verbosity= high,
>>> 
>>> /
>>> 
>>> &system
>>> 
>>>    a= 23.8688, b= 11.1968, c= 7.8252, cosab= 0.417083157,
>space_group = 15,
>>> 
>>>    nat=  20, ntyp= 4,
>>> 
>>>    ecutwfc =15.0,
>>> 
>>>    rhombohedral= .false.
>>> 
>>> /
>>> 
>>> &electrons
>>> 
>>>    diagonalization='david'
>>> 
>>>    mixing_beta = 0.7
>>> 
>>>    conv_thr= 1.0e-7
>>> 
>>> /
>>> 
>>> &ions
>>> 
>>> ion_dynamics='bfgs'
>>> 
>>> /
>>> 
>>> ATOMIC_SPECIES
>>> 
>>> Zr 91.224 Zr.pbe-mt_fhi.UPF
>>> 
>>> C 12.010 C.pbe-mt_fhi.UPF
>>> 
>>> O 16.00  O.pbe-mt_fhi.UPF
>>> 
>>> H 1.00   H.pbe-mt_fhi.UPF
>>> 
>>> ATOMIC_POSITIONS crystal_sg
>>> 
>>> Zr      0.8055700   0.2260400   0.1404400
>>> 
>>> O       0.7837400   0.2764700   0.3778600
>>> 
>>> O       0.7887800   0.0352700   0.0965300
>>> 
>>> O       0.8863700   0.2930100   0.0648300
>>> 
>>> O       0.7894200   0.4193200   0.0923400
>>> 
>>> O       0.8721000   0.1295600  -0.7030000
>>> 
>>> C       0.8994700   0.1401400   0.4427600
>>> 
>>> C       0.9514400   0.0679000   0.4731700
>>> 
>>> C       0.9682300  -0.0035900   0.3401200
>>> 
>>> C       0.0168300  -0.0717400   0.3668600
>>> 
>>> C      -0.2965000  -0.2104000  -0.0790000
>>> 
>>> C      -0.7034500  -0.6656900   0.0788000
>>> 
>>> H       0.9426100  -0.0042000   0.2174500
>>> 
>>> H       0.0307000   0.8716500   0.2661000
>>> 
>>> H       0.3320300   0.3845300   0.1396500
>>> 
>>> H       0.6681300   0.8400300   0.8596200
>>> 
>>> C       0.7500000   0.4711800   0.0000000
>>> 
>>> C       0.7500000   0.9838200   0.0000000
>>> 
>>> C       0.7500000   0.8516100   0.0000000
>>> 
>>> C       0.7500000   0.6036500   0.0000000
>>> 
>>> 
>>> Can you tell me where I am making a mistake??
>>> thanks a lot
>>> dearly
>>> lorenzo
>>> 
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at 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 at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 8 Jun 2016 16:23:51 -0400
>From: Manu Hegde <mhegde at uwaterloo.ca>
>Subject: [Pw_forum] Regarding ph.x
>To: pw_forum <pw_forum at pwscf.org>
>Message-ID:
>	<CA+g44DvSiAHSKnwn-_Swmv9zUp-C4OAWj1r4Z-euFDekFvhhmA at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hello All,
>
>I was trying to calculate phonon dispersion in PbTIO3, my SCF
>calculations
>went well, but I am struggling with ph.x. It is taking long time to
>converge. Any suggestions to  improve the input and make it faster?.
>
> Both SCF and Phonon input are below, please have a look.
>
>
>&CONTROL
>                 calculation = 'scf' ,
>                restart_mode = 'from_scratch' ,
>                      outdir = '/home/user/espresso-5.3.0/PBTIO/' ,
>                  pseudo_dir = '/home/user/espresso-5.3.0/pseudo/' ,
>                      prefix = 'perov',
>                          tstress = .true.,
>                         tprnfor = .true.,
>                       verbosity = 'high',
> /
> &SYSTEM
>
>                           A = 3.97,
>                       space_group = 221,
>                         nat = 3,
>                        ntyp = 3,
>                     ecutwfc = 30.0 ,
>
> /
> &ELECTRONS
>                    conv_thr = 1D-6,
>                   mixing_beta=0.3
> /
>ATOMIC_SPECIES
>   Pb  207.20000  Pb.pz-d-van.UPF
>   Ti   47.86700  Ti.pz-sp-van_ak.UPF
>    O   15.99940  O.pz-van_ak.UPF
>ATOMIC_POSITIONS crystal_sg
>   Pb  1a
>   Ti  1b  0.5
>    O  0.5 0.5 0.0
>K_POINTS automatic
>  8 8 8   0 0 0
>
>
>Phonon input
>
>
>phonons of PbTio at grid
>&inputph
>        prefix = 'perov'
>
>        ldisp = .true.,
>        fildyn = 'pbtio.dyn',
>        amass(1) = 207.2,
>        amass(2) = 47.867,
>        amass(3) = 15.9994
>        outdir = '/home/user/espresso-5.3.0/PBTIO/'
>        nq1 = 4,
>        nq2 = 4,
>        nq3 = 4,
>        tr2_ph = 1.0d-12,
>/
>
>
>
>Thanks and Regards,
>Manu
>University of Waterloo
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>------------------------------
>
>Message: 6
>Date: Wed, 8 Jun 2016 23:52:22 +0300
>From: Bahad?r SALMANKURT <bsalmankurt at gmail.com>
>Subject: Re: [Pw_forum] Regarding ph.x
>To: PWSCF Forum <pw_forum at pwscf.org>
>Message-ID:
>	<CADT9cuvgUdQy2HPdjDGeYhJJMz6GKQ8OQ13Q=d2VgodaEQxApg at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Dear Manu,
>
>Increasing ecut may be useful. Also conv_thr is high, reduce it to
>1D-10
>which is good for phonon calculation. For &inputph, add the following;
>
>*alpha_mix(1) = 0.3 *
>
>I always use alpha_mix(1) as 0.3 or 0.5 when I have converge problem.
>Default
>value is 0.7.
>
>Bests
>
>
>
>2016-06-08 23:23 GMT+03:00 Manu Hegde <mhegde at uwaterloo.ca>:
>
>> Hello All,
>>
>> I was trying to calculate phonon dispersion in PbTIO3, my SCF
>calculations
>> went well, but I am struggling with ph.x. It is taking long time to
>> converge. Any suggestions to  improve the input and make it faster?.
>>
>>  Both SCF and Phonon input are below, please have a look.
>>
>>
>> &CONTROL
>>                  calculation = 'scf' ,
>>                 restart_mode = 'from_scratch' ,
>>                       outdir = '/home/user/espresso-5.3.0/PBTIO/' ,
>>                   pseudo_dir = '/home/user/espresso-5.3.0/pseudo/' ,
>>                       prefix = 'perov',
>>                           tstress = .true.,
>>                          tprnfor = .true.,
>>                        verbosity = 'high',
>>  /
>>  &SYSTEM
>>
>>                            A = 3.97,
>>                        space_group = 221,
>>                          nat = 3,
>>                         ntyp = 3,
>>                      ecutwfc = 30.0 ,
>>
>>  /
>>  &ELECTRONS
>>                     conv_thr = 1D-6,
>>                    mixing_beta=0.3
>>  /
>> ATOMIC_SPECIES
>>    Pb  207.20000  Pb.pz-d-van.UPF
>>    Ti   47.86700  Ti.pz-sp-van_ak.UPF
>>     O   15.99940  O.pz-van_ak.UPF
>> ATOMIC_POSITIONS crystal_sg
>>    Pb  1a
>>    Ti  1b  0.5
>>     O  0.5 0.5 0.0
>> K_POINTS automatic
>>   8 8 8   0 0 0
>>
>>
>> Phonon input
>>
>>
>> phonons of PbTio at grid
>> &inputph
>>         prefix = 'perov'
>>
>>         ldisp = .true.,
>>         fildyn = 'pbtio.dyn',
>>         amass(1) = 207.2,
>>         amass(2) = 47.867,
>>         amass(3) = 15.9994
>>         outdir = '/home/user/espresso-5.3.0/PBTIO/'
>>         nq1 = 4,
>>         nq2 = 4,
>>         nq3 = 4,
>>         tr2_ph = 1.0d-12,
>> /
>>
>>
>>
>> Thanks and Regards,
>> Manu
>> University of Waterloo
>>
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>-- 
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>Bahad?r SALMANKURT
>Ph.D. Candidate
>Department of Physics, Sakarya University, TURKEY
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