[Pw_forum] Pw_forum Digest, Vol 40, Issue 20
Tram Bui
trambui at u.boisestate.edu
Thu Oct 14 21:14:57 CEST 2010
Hi,
My name is Tram Bui and i'm new to the forum so i'm not quite sure how the
Q&A work, but today I want to try the forum with my very first question is
that: If i want to calculate the total energy based on lattice parameters of
SiC, how do you determine (or find) the ecutoff (kinetic energy cutoff of
wave function) value for a material structure such as SiC?
Thank you,
Tram
On Wed, Oct 13, 2010 at 4:54 AM, Shyam Khambholja <physik.shyam at gmail.com>wrote:
> 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
>> 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
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Tram Bui
B.S. Materials Science & Engineering
trambui at u.boisestate.edu
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