[Pw_forum] Pw_forum Digest, Vol 85, Issue 27
Chukwu Jonathan
chuxjoh at gmail.com
Sat Aug 30 22:05:53 CEST 2014
Thank you Dr. Axel Kohlmeyer for your link.
I know it will be of great help
Chukwu Jonathan
On Fri, Aug 29, 2014 at 3:00 AM, <pw_forum-request at pwscf.org> wrote:
> Send Pw_forum mailing list submissions to
> pw_forum at pwscf.org
>
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> or, via email, send a message with subject or body 'help' to
> pw_forum-request at pwscf.org
>
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> pw_forum-owner at pwscf.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pw_forum digest..."
>
>
> Today's Topics:
>
> 1. pp.x (Masoud Avi)
> 2. space group bug? (Tommaso Francese)
> 3. Re: space group bug? (Vincenzo Verdolino)
> 4. Re: Pw_forum Digest, Vol 85, Issue 22 (Chukwu Jonathan)
> 5. Re: Pw_forum Digest, Vol 85, Issue 22 (Axel Kohlmeyer)
> 6. Re: Fwd: Band calculation gets terminated (Aditya Putatunda)
> 7. Re: pp.x (Paolo Giannozzi)
> 8. running PWSCF on IB-based cluster (??)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 28 Aug 2014 20:34:04 +0430
> From: Masoud Avi <masoud.avi at gmail.com>
> Subject: [Pw_forum] pp.x
> To: pw_forum at pwscf.org
> Message-ID:
> <CAC4vesExcXXm48Rrx8kf2u-=
> 53sceVmROZaPNH+ko9AMKi_QVg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi dear all
> I want to calculation total valence charge density of my composition withe
> pp.x code, for a typical plane and special direction and special state,
> For example:
> The total valence charge density without including d band for the X state,
> in the plane(1 -1 0) and along the<1 1 1> direction.
> I know how define the plane, but I dont know that how to other define,
>
> please help me
>
> masoud alavi
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> ------------------------------
>
> Message: 2
> Date: Thu, 28 Aug 2014 18:50:37 +0200
> From: Tommaso Francese <neutrinofrancese at gmail.com>
> Subject: [Pw_forum] space group bug?
> To: pw_forum at pwscf.org
> Message-ID: <C33B3242-7727-4F89-AB43-1E1DDB918FC9 at gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear all QE users,
> i tried to simulate a crystal structure of silicon with symmetry space
> group Fd-3m, where the input was:
>
> &CONTROL
> calculation = 'scf' ,
> outdir = '/home/***/espresso-5.1/tmp/' ,
> pseudo_dir = '/home/***/upf_files/' ,
> prefix = 'si' ,
> /
> &SYSTEM
> ibrav = 2,
> A = 5.43 ,
> B = 5.43 ,
> C = 5.43 ,
> cosAB = 0 ,
> cosAC = 0 ,
> cosBC = 0 ,
> nat = 8,
> ntyp = 1,
> ecutwfc = 60 ,
> /
> &ELECTRONS
> /
> ATOMIC_SPECIES
> Si 28.08550 Si.pz-vbc.UPF
> ATOMIC_POSITIONS crystal
> Si 0.000000000 0.000000000 0.000000000
> Si -0.000000000 0.500000000 0.500000000
> Si 0.500000000 0.500000000 0.000000000
> Si 0.500000000 -0.000000000 0.500000000
> Si 0.750000000 0.250000000 0.750000000
> Si 0.250000000 0.250000000 0.250000000
> Si 0.250000000 0.750000000 0.750000000
> Si 0.750000000 0.750000000 0.250000000
> K_POINTS automatic
> 1 1 1 1 1 1
>
> i don?t know why, but when i try to visualize both the Input file and
> Output file with XcrySden or J-ICE, the structure which shown is completely
> different from the structure introduced, resulting with a=b=c= 3.84
> Angstroms instead of being 5.43, and the angles alpha=beta=gamma= 60?,
> instead of being 90?.
>
> Does anyone know why it happens? Is it an internal bug?
>
> I attach also the output, saw you can see directly what happens.
>
> Thanks in andvance,
> Tommaso Francese,
> Universit? C? Foscari di Venezia.
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 28 Aug 2014 19:18:36 +0200
> From: Vincenzo Verdolino <vincenzo.verdolino at gmail.com>
> Subject: Re: [Pw_forum] space group bug?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <E56EE1D0-5A40-4F06-8BA7-DBF035F5C340 at gmail.com>
> Content-Type: text/plain; charset=utf-8
>
> It is not a bug. If you check your input file and you change the
> ireducible zone representation you should look at your input original
> structure. If you run an scf calculation and you look at the output you
> have a changed representation which is by default the minimal one. If you
> carefully look at the atomic distances you will find your cell parameters.
>
> I know it's quite annoing :-) but you get used to
>
> Sent from my iPhone
>
> > On 28/ago/2014, at 18:50, Tommaso Francese <neutrinofrancese at gmail.com>
> wrote:
> >
> > Dear all QE users,
> > i tried to simulate a crystal structure of silicon with symmetry space
> group Fd-3m, where the input was:
> >
> > &CONTROL
> > calculation = 'scf' ,
> > outdir = '/home/***/espresso-5.1/tmp/' ,
> > pseudo_dir = '/home/***/upf_files/' ,
> > prefix = 'si' ,
> > /
> > &SYSTEM
> > ibrav = 2,
> > A = 5.43 ,
> > B = 5.43 ,
> > C = 5.43 ,
> > cosAB = 0 ,
> > cosAC = 0 ,
> > cosBC = 0 ,
> > nat = 8,
> > ntyp = 1,
> > ecutwfc = 60 ,
> > /
> > &ELECTRONS
> > /
> > ATOMIC_SPECIES
> > Si 28.08550 Si.pz-vbc.UPF
> > ATOMIC_POSITIONS crystal
> > Si 0.000000000 0.000000000 0.000000000
> > Si -0.000000000 0.500000000 0.500000000
> > Si 0.500000000 0.500000000 0.000000000
> > Si 0.500000000 -0.000000000 0.500000000
> > Si 0.750000000 0.250000000 0.750000000
> > Si 0.250000000 0.250000000 0.250000000
> > Si 0.250000000 0.750000000 0.750000000
> > Si 0.750000000 0.750000000 0.250000000
> > K_POINTS automatic
> > 1 1 1 1 1 1
> >
> > i don?t know why, but when i try to visualize both the Input file and
> Output file with XcrySden or J-ICE, the structure which shown is completely
> different from the structure introduced, resulting with a=b=c= 3.84
> Angstroms instead of being 5.43, and the angles alpha=beta=gamma= 60?,
> instead of being 90?.
> >
> > Does anyone know why it happens? Is it an internal bug?
> >
> > I attach also the output, saw you can see directly what happens.
> >
> > Thanks in andvance,
> > Tommaso Francese,
> > Universit? C? Foscari di Venezia.
> >
> > <silicon.pw.out>
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 Aug 2014 11:50:42 -0700
> From: Chukwu Jonathan <chuxjoh at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 85, Issue 22
> To: pw_forum at pwscf.org
> Message-ID:
> <
> CAM_gj_ZjxCrjQetYatSxfedYa78vFUURaJJJgjHfTd3bY3BmSw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> My calculation is QE and I am using it to solve problems on Molecular
> Dynamics (MD). Please do we have anyone working on MD to put me through?
> Thank you
>
>
> On Sun, Aug 24, 2014 at 3:00 AM, <pw_forum-request at pwscf.org> wrote:
>
> > Send Pw_forum mailing list submissions to
> > pw_forum at pwscf.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://pwscf.org/mailman/listinfo/pw_forum
> > or, via email, send a message with subject or body 'help' to
> > pw_forum-request at pwscf.org
> >
> > You can reach the person managing the list at
> > pw_forum-owner at pwscf.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > Today's Topics:
> >
> > 1. QE-GPU (Chukwu Jonathan)
> > 2. Re: C6 unit (Mohamad Moadeli)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 23 Aug 2014 08:35:44 -0700
> > From: Chukwu Jonathan <chuxjoh at gmail.com>
> > Subject: [Pw_forum] QE-GPU
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <
> > CAM_gj_b1qSiR_QR-LnPM8h8KUuHFFERP4bhGSVNozJrokSbLxg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > My name is Jonathan, I am a new member in this forum.
> > I want start using the the quantum espresso my PhD research work.
> > kindly assist me on how to start solving problems with the code.
> > Thank you.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
> http://pwscf.org/pipermail/pw_forum/attachments/20140823/f66e7fca/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sun, 24 Aug 2014 13:36:14 +0430
> > From: Mohamad Moadeli <mohammad.moaddeli at gmail.com>
> > Subject: Re: [Pw_forum] C6 unit
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID:
> > <
> > CANfJyHS1zxsxfjsdiEoy_PFZUswO9-jEr-dnxPzps1mDdfRSAw at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you so much
> >
> >
> > On Tue, Aug 19, 2014 at 1:29 AM, Paolo Giannozzi <
> paolo.giannozzi at uniud.it
> > >
> > wrote:
> >
> > > On Sun, 2014-08-17 at 23:27 +0430, Mohamad Moadeli wrote:
> > > >
> > > > I am doing calculations with QE and I am trying to use DFT-D for a
> > > > combined system, but I do not know what the unit of C6 coefficient
> is?
> > > > (as implemented)
> > >
> > > from the Modules/mm_dispersion.f90 file:
> > >
> > > ! vdw C6 and radii for the first 86 atoms for the DFTD2 method
> > > ! Data from the DFT-D2 section of the dftd3.f file found on
> > > S.Grimme's home page:
> > > !
> > >
> > >
> >
> http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3
> > > ! See also S. Grimme, J. Comp. Chem., 27, 1787 (2006)
> > > ! First column: C6, converted to Ry*Bohr^6 units
> > > ! (in the paper: J*nm^6/mol, conversion factor: 1 J*nm^6/mol =
> > > 34.69 Ry*Bohr^6)
> > > ! Second column: radii, in Bohr (in the paper they are in A)
> > > !
> > > DATA vdw_coeffs / &
> > > 4.857, 1.892,&
> > > ...
> > >
> > > P.
> > >
> > > --
> > > Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> > > 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
> > >
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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 85, Issue 22
> > ****************************************
> >
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> ------------------------------
>
> Message: 5
> Date: Thu, 28 Aug 2014 14:59:43 -0400
> From: Axel Kohlmeyer <akohlmey at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 85, Issue 22
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CADTmJ6HGioqz46VrH49VA__gJ=
> DAKh5k-r3NFKXT2wggzjkrcg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Thu, Aug 28, 2014 at 2:50 PM, Chukwu Jonathan <chuxjoh at gmail.com>
> wrote:
> > My calculation is QE and I am using it to solve problems on Molecular
> > Dynamics (MD). Please do we have anyone working on MD to put me through?
>
> that is far too generic a question to help you with. how to run an MD
> is not explained in a few words. please keep in mind that a mailing
> list is no replacement for an adviser, textbooks or a tutorial.
>
> specific QE tutorial materials are available here:
> http://www.quantum-espresso.org/tutorials/
> there also is the documentation and FAQ.
>
> axel.
>
>
> > Thank you
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 29 Aug 2014 10:29:56 +0530
> From: Aditya Putatunda <adityaputatunda at gmail.com>
> Subject: Re: [Pw_forum] Fwd: Band calculation gets terminated
> To: PWSCF Forum <pw_forum at pwscf.org>, Trinh.Vo at jpl.nasa.gov
> Message-ID:
> <CANbmZMAyGnp7MbyJ+=
> DwAN5UKaMB-XUv+uK7ZQdYx1uufE4Juw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Trinh,
> Thanks once again for your reply. Actually I knew from my
> system-admin that my machine is quadsocket 64 core shared memory theory
> workstation with 16 processors per socket. In simple terms, you may say the
> machine I am using has only one node where all the 64 processors access the
> same memory (it's just like a big computer with 64 processors). So please
> suggest me a way to solve this as I am new to QE.
>
> Thanks,
> Aditya
>
>
> On Wed, Aug 27, 2014 at 5:58 PM, Aditya Putatunda <
> adityaputatunda at gmail.com
> > wrote:
>
> > Hi all,
> > Thanks a lot for your replies. I am attaching the input files as
> > you asked. I can send the output files too in case you need them.
> >
> >
> > Thanks,
> > Aditya
> >
> >
> > On Wed, Aug 27, 2014 at 2:04 AM, Vo, Trinh (398C) <Trinh.Vo at jpl.nasa.gov
> >
> > wrote:
> >
> >> Hi Aditya,
> >>
> >> I have similar problem before with a nscf run. I finally found out
> >> that it was due to bus problem, since my job was very big. I reduced
> the
> >> number of CPUs per node (and of course increased number of nodes), then
> it
> >> worked. You may try it again with this way to see if it solves your
> >> problem.
> >>
> >> Trinh
> >>
> >> From: Aditya Putatunda <adityaputatunda at gmail.com>
> >> Reply-To: PWSCF Forum <pw_forum at pwscf.org>
> >> Date: Tuesday, August 26, 2014 9:28 AM
> >> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> >> Subject: [Pw_forum] Fwd: Band calculation gets terminated
> >>
> >> Hello all,
> >> Sorry to state, but I got no reply. I am still getting the same error
> >> while doing nscf for the DOS calculations. Please help me figure out the
> >> problem why the application terminates without putting the JOB DONE
> quote.
> >> Moreover I cannot use the results further for plotting the DOS.
> >>
> >> Thanks,
> >> Aditya
> >>
> >> ---------- Forwarded message ----------
> >> From: Aditya Putatunda <adityaputatunda at gmail.com>
> >> Date: Thu, Aug 21, 2014 at 8:46 AM
> >> Subject: Band calculation gets terminated
> >> To: pw_forum at pwscf.org
> >>
> >>
> >> Hi all,
> >> I was doing a bands calculation for a non-metallic system of about 60
> >> atoms. But each time the pw.x process terminates with the last line "
> >> Writing output data file *filename*.save " in the bands.out file.
> Now
> >> further when I try to collect the bands calculated by pw.x using
> bands.x,
> >> the process terminated abruptly with no CRASH file. Also the temp files
> are
> >> quite large ( >750Mb).
> >>
> >> I am using parallel version 5.0.1 on 48 processors and have no
> >> disk/memory issues in my workstation. Has someone come across this
> problem
> >> or is it some system/machine specific error. Please enlighten me.
> >>
> >> -Aditya
> >> NISER, Bhubaneswar,
> >> India
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >
> >
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> ------------------------------
>
> Message: 7
> Date: Fri, 29 Aug 2014 11:23:50 +0200
> From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
> Subject: Re: [Pw_forum] pp.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1409304230.3643.2.camel at fe12lx.fisica.uniud.it>
> Content-Type: text/plain; charset="UTF-8"
>
> What can be done is explained in the documentation of the pp.x
> code (PP/Doc/INPUT_PP.*). If you need something special, you
> have to implement it.
>
> P.
>
> On Thu, 2014-08-28 at 20:34 +0430, Masoud Avi wrote:
> > Hi dear all
> > I want to calculation total valence charge density of my composition
> > withe pp.x code, for a typical plane and special direction and special
> > state,
> > For example:
> > The total valence charge density without including d band for the X
> > state, in the plane(1 -1 0) and along the<1 1 1> direction.
> > I know how define the plane, but I dont know that how to other define,
> >
> >
> > please help me
> >
> >
> > masoud alavi
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 29 Aug 2014 17:53:35 +0800 (GMT+08:00)
> From: ?? <xinggao at impcas.ac.cn>
> Subject: [Pw_forum] running PWSCF on IB-based cluster
> To: pw_forum at pwscf.org
> Message-ID: <1b829ab.b45d.148212f358e.Coremail.xinggao at impcas.ac.cn>
> Content-Type: text/plain; charset="gbk"
>
>
> Dear QE community,
>
> We have an infini-band based cluster with 8 computing nodes and each nodes
> contains 16 cores. I compiled QE package on this cluster successfully with
> compiler mpif90 (openmpi intel compiler) and there was no problem to run
> pw.x on one node with 16 processors. However, when I tried to use two nodes
> (that is, -np 32), I met "processor affinity failure". It says, "an attempt
> to set processor affinity has failed - please check to ensure that your
> system supports such functionality. If so, then this is probably something
> that should be reported to the OMPI developers". Actually, there is no such
> problem when I run other program. I am wondering if someone else met the
> similar question before? And please give me any hint which may help me on
> this problem! Thanks in advance!
>
> Best,
>
> Xing
>
>
>
>
>
>
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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 85, Issue 27
> ****************************************
>
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