[Pw_forum] Pw_forum Digest, Vol 40, Issue 20
Shyam Khambholja
physik.shyam at gmail.com
Wed Oct 13 12:54:41 CEST 2010
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:
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> 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
> >>
> >
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> >
> > End of Pw_forum Digest, Vol 40, Issue 19
> > ****************************************
> >
>
>
>
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> ------------------------------
>
> 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
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> 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
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>
> 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
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