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 > > 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. 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140828/03fb7218/attachment-0001.html > > ------------------------------ > > 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. > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: silicon.pw.out > Type: application/octet-stream > Size: 11379 bytes > Desc: not available > Url : > http://pwscf.org/pipermail/pw_forum/attachments/20140828/0752e8da/attachment-0001.obj > > ------------------------------ > > 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... > > URL: > > > 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 > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > > http://pwscf.org/pipermail/pw_forum/attachments/20140824/f764e49c/attachment-0001.html > > > > ------------------------------ > > > > _______________________________________________ > > 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 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140828/44a6874f/attachment-0001.html > > ------------------------------ > > 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 > >> > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140829/cc9a9358/attachment-0001.html > > ------------------------------ > > 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 > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20140829/9d9b97cf/attachment-0001.html > > ------------------------------ > > _______________________________________________ > 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 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140830/6932df92/attachment.html