[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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>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
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
>--
>
>Bahad?r SALMANKURT
>Ph.D. Candidate
>Department of Physics, Sakarya University, TURKEY
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>------------------------------
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://pwscf.org/mailman/listinfo/pw_forum
>
>End of Pw_forum Digest, Vol 107, Issue 9
>****************************************
--
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