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