Thank you Prof. Stefano, how to calculate energy of an isolated atom ?
shyam On Wed, Oct 13, 2010 at 2:32 PM, <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://www.democritos.it/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. Re: Pw_forum Digest, Vol 40, Issue 19 (matteo calandra) > 2. cohesive energy (Shyam Khambholja) > 3. Re: Question about Young's modulus (Mahdi Mirnezhad) > 4. Re: Question about Young's modulus (Stefano de Gironcoli) > 5. Re: cohesive energy (Stefano de Gironcoli) > 6. pw.x crash on LSF/mvapich (Kiss, Ioan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 12 Oct 2010 10:14:42 +0200 > From: matteo calandra <matteo.calandra at impmc.jussieu.fr> > Subject: Re: [Pw_forum] Pw_forum Digest, Vol 40, Issue 19 > To: pw_forum at pwscf.org > Message-ID: <20101012101442.84091vx35nxcb3zm at www1.impmc.upmc.fr> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear Min Wu, > > I think you should sit down a bit and try to solve this issue > by yourself. This is not a problem concerning the code as you would have > the same problem with any other code, but it concerns basic > physics and group theory. > In the future we plan to write a program to find the isotropic cross > section > with the sallest number of calculations possible from the knowledge of > the symmetries of the lattice. > However this is not yet done (I am not aware of any program doing this). > > So, as I always do in these case, you should si down,try to understand > Ch. Bouder's paper and find the polarization vectors necessary to > obtain the isotropic cross section. > > M. > > > > > Message: 6 > > Date: Tue, 12 Oct 2010 14:59:33 +0800 > > From: "wumindt2" <wumindt2 at zju.edu.cn> > > Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > > To: pw_forum at pwscf.org > > Message-ID: <CTFHHDRTTMMZGMEUQITYAFBYXCPW.wumindt2 at zju.edu.cn> > > Content-Type: text/plain; charset="gb2312" > > > > Dear Matteo, > > > > Thanks for the information, i read the C. Brouder the paper a little bit. > > I'am still not sure how to choose the polarization vector. > > For instance, we have a crystal with spacegroup of P42/MNM, point > > group of 4/mmm. > > According to the Table in C. Brouder's paper, this is a dichroism > compound. > > Thus, how can we choose the polarization vector when calculating the XAS > > of this compound? > > Can you please show me how? > > > > Thanks so much! > > > > Cheers, > > > > Min Wu > > 2010-10-12 > > > > > >> From: Matteo Calandra <matteo.calandra at impmc.jussieu.fr> > >> Reply-To: PWSCF Forum <pw_forum at pwscf.org> > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > >> Date: Mon, 11 Oct 2010 10:08:16 +0200 > >> > >> Dear > >> > >> I assume you are talking of the dipolar part only. > >> For the quadrupolar it is substantially more complicate. > >> The number of independent calculations that you have > >> to perform to obtain the isotropic cross section (powder) > >> depends on the point group of the space group > >> of your crystal. > >> It is 1 for a cubic or tetraedric crystal, > >> 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial > >> (ot trichroic) crystal. > >> I suggest you read > >> C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 > >> for more details. > >> > >> M. > >> > >> > >>> > >>> Message: 3 > >>> Date: Sat, 09 Oct 2010 22:48:53 +0800 > >>> From: "wumindt2" > > > >>> Subject: Re: [Pw_forum] Xspectra calculation > >>> To: pw_forum at pwscf.org > >>> Message-ID: > > > >>> Content-Type: text/plain; charset="gb2312" > >>> > >>> Dear matteo, > >>> > >>> Thanks. > >>> > >>> For dichroism compound, do we just need the in-plane and the c-axis > >>> polarization vectors? > >>> While for trichroism compound, do we need to calculate three different > >>> polarization vectors? > >>> Am i right? > >>> > >>> Best regards, > >>> > >> _______________________________________________ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > ------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > End of Pw_forum Digest, Vol 40, Issue 19 > > **************************************** > > > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 Oct 2010 17:36:25 +0700 > From: Shyam Khambholja <physik.shyam at gmail.com> > Subject: [Pw_forum] cohesive energy > To: pw_forum at pwscf.org > Message-ID: > <AANLkTimSwcsJ1VosFZGQSotksAiHyV_c6SqfycreAmHd at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > scf calculation can give us total energy. but how to calculate > cohesive energy of elements like aluminium from total energy ? thanks in > advance > > -- > Mr. Shyam G Khambholja > Research student, > Depratment of Physics, > Sardar Patel University, Gujarat > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101012/8cf3d73e/attachment.html > > ------------------------------ > > Message: 3 > Date: Tue, 12 Oct 2010 16:25:00 +0330 > From: Mahdi Mirnezhad <mirnezhad.mm at gmail.com> > Subject: Re: [Pw_forum] Question about Young's modulus > To: pw_forum <pw_forum at pwscf.org> > Message-ID: > <AANLkTi=pVPvpNDn2mZiUyG7U9Nd6i2NuPj93zXUJQrO=@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Developers, > I think there is a problem in the calculation of stress in Quantum > Esperesso. This problem concern with the volume of unit cell. For bulk > structures there is no problem for determination of Volume but in the > super cell method code calculate stress according to unit cell volume > so when i calculate Young's Modulus for graphene with two method > (strees/strain or (E=(1/V)*second derivative of energy) ) i get > different answer. > What is your suggestion? > Thanks for your reply. > > Mahdi Mirnezhad > Msc student of Mechanics > Guilan University. > > > > On 10/7/10, Mahdi Mirnezhad <mirnezhad.mm at gmail.com> wrote: > > Dear all, > > I calculated Young's modulusfor graphene and i got correct answer but > > when I want to calculate Young's modulus for CNT(3,3) for a axial > > strain with the same condition (same PS) i got a wrong answer? > > Any suggestion appreciated, > > tanks > > > > mahdi mirnezhade > > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Oct 2010 15:01:29 +0200 > From: Stefano de Gironcoli <degironc at sissa.it> > Subject: Re: [Pw_forum] Question about Young's modulus > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4CB45C29.6070908 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > for a 2-D system I guess that the definition of stress will involve the > area and not the volume ... > stefano > > > Mahdi Mirnezhad wrote: > > Dear Developers, > > I think there is a problem in the calculation of stress in Quantum > > Esperesso. This problem concern with the volume of unit cell. For bulk > > structures there is no problem for determination of Volume but in the > > super cell method code calculate stress according to unit cell volume > > so when i calculate Young's Modulus for graphene with two method > > (strees/strain or (E=(1/V)*second derivative of energy) ) i get > > different answer. > > What is your suggestion? > > Thanks for your reply. > > > > Mahdi Mirnezhad > > Msc student of Mechanics > > Guilan University. > > > > > > > > On 10/7/10, Mahdi Mirnezhad <mirnezhad.mm at gmail.com> wrote: > > > >> Dear all, > >> I calculated Young's modulusfor graphene and i got correct answer but > >> when I want to calculate Young's modulus for CNT(3,3) for a axial > >> strain with the same condition (same PS) i got a wrong answer? > >> Any suggestion appreciated, > >> tanks > >> > >> mahdi mirnezhade > >> > >> > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Oct 2010 15:07:28 +0200 > From: Stefano de Gironcoli <degironc at sissa.it> > Subject: Re: [Pw_forum] cohesive energy > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4CB45D90.9030502 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > the cohesive energy is the energy per atom of the bulk minus the energy > of an isolated atom. > stefano > > Shyam Khambholja wrote: > > Hello all, > > scf calculation can give us total energy. but how to > calculate > > cohesive energy of elements like aluminium from total energy ? thanks in > > advance > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 12 Oct 2010 18:02:00 +0000 > From: "Kiss, Ioan" <kissi at uni-mainz.de> > Subject: [Pw_forum] pw.x crash on LSF/mvapich > To: "pw_forum at pwscf.org" <pw_forum at pwscf.org> > Message-ID: > < > C2A03FEA95390F46839DC92BB46F57741D19C449 at e14mdb-01.zdv.Uni-Mainz.DE> > Content-Type: text/plain; charset="iso-8859-1" > > Dear PWSCF users and developers, > > I have a problem running pw.x in our computer center. > The MPI environment is mvapich_1.1, the queuing system is LSF, and I have > compiled PWSCF with the Intel compiler suite together with MKL libraries. > The threading via MKL is turned off by exporting OMP_NUM_THREADS=1. > The machines are 8 core Xeons with QDR Infiniband and 48GB of ECC > memory/node. > > I would like to perform some geometry optimizations on Cd doped > CuInSe2 with PWSCF version 4.1.2. > The FFT grid for the respective slab is 150:150:144, and it does run > on 24 CPUs (i.e. 3 nodes with 8 cores). > However, by taking the same binary and input file, if I would like to use > 48, 72 > or 144 CPU cores, than the job will crash right after the WFC > initialization: > > Self-consistent Calculation > > iteration # 1 ecut= 25.00 Ry beta=0.70 > Davidson diagonalization with overlap > Signal 15 received. > . > . > . > Signal 15 received. > Job /usr/local/lsf/7.0/linux2.6-glibc2.3-x86_64/bin/mvapich_wrapper > VIADEV_USE_SHMEM_ALLREDUCE=0 > VIADEV_USE_SHMEM_REDUCE=0 VIADEV_USE_SHMEM_BARRIER=0 > DISABLE_RDMA_ALLTOALL=1 > DISABLE_RDMA_ALLGATHER=1 DISABLE_RDMA_BARRIER=1 > MV2_CPU_MAPPING=0:1:2:3:4:5:6:7 ./pwTest.x -in INP-PWSCF > > TID HOST_NAME COMMAND_LINE STATUS > TERMINATION_TIME > ===== ========== ================ ======================= > =================== > 00000 moment1 /usr/local/lsf/l Exit (1) 10/12/2010 > 19:20:36 > . > . > . > 00001 moment1 /usr/local/lsf/l Exit (174) 10/12/2010 > 19:20:36 > > As you can see, I have already tried to deactivate the shared memory > optimizations > implemented in mvapich in the Nemesis routines, but that did not help > either. > Strangely, on the same machine I can run CPMD without any issues, so I am > really wondering > what I am doing wrong or what should I change to fix this problem. I have > tried several different > MKL versions and so forth, but to be honest it seems to me that I just > cannot fix it. > Also, using the same input file and 48-72 CPUs the job will nicely finish > in Juelich supercomputer > center and also in the department's tiny local cluster running OpenMPI. > > Do you have some ideas why the machine under LSF/mvapich is not fully > cooperating with > PWSCF above 24 CPU cores, or what should be done to remedy this issue? > > > Thanks in advance for any helpful comment, > > Janos. > > > ========================================== > Dr. Janos Kiss e-mail: kissi at uni-mainz.de > Johannes Gutenberg-Universitaet > Institut f. Anorg. u. Analyt. Chemie > AK Prof. Dr. Claudia Felser > Staudinger Weg 9 / Raum 01-230 > 55128 Mainz/ Germany > Phone: +49-(0)6131-39-22703 > Fax: +49-(0)6131-39-26267 > Web: http://www.superconductivity.de/ > ========================================= > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 40, Issue 20 > **************************************** > -- Mr. Shyam G Khambholja Reseach student, Depratment of Physics, Sardar Patel University, Gujarat Cell No. : +91 999 888 3867 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101013/8e5430ed/attachment-0001.htm