Der prof. Paolo,<br>
<br>
Thanks very much to your reply. <br>
<br>
1. Re: ion_radius (Paolo Giannozzi)<br>
<br>
WANG Riping <br>
2010.12.27<br>
<br><br><div class="gmail_quote">On 25 December 2010 12:36, <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: ion_radius (Paolo Giannozzi)<br>
2. how does the calculation scales with number of processors<br>
(mohnish pandey)<br>
3. Re: how does the calculation scales with number of processors<br>
(Stefano de Gironcoli)<br>
4. Re: how does the calculation scales with number of processors<br>
(mohnish pandey)<br>
5. Re: how does the calculation scales with number of processors<br>
(Paolo Giannozzi)<br>
6. Merry Christmas (jiayudai)<br>
7. About the difference between the energy obtained from<br>
geometry optimization and single energy calculation. (Hongsheng Zhao)<br>
8. About the relationship between enthalpy and pressure.<br>
(Hongsheng Zhao)<br>
9. Re: About the relationship between enthalpy and pressure.<br>
(Stefano de Gironcoli)<br>
10. Re: About the difference between the energy obtained from<br>
geometry optimization and single energy calculation. (Prasenjit Ghosh)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 24 Dec 2010 09:56:00 +0100<br>
From: Paolo Giannozzi <<a href="mailto:giannozz@democritos.it">giannozz@democritos.it</a>><br>
Subject: Re: [Pw_forum] ion_radius<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:5B32AABF-A8DA-4C29-8850-9250578A7450@democritos.it">5B32AABF-A8DA-4C29-8850-9250578A7450@democritos.it</a>><br>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed<br>
<br>
<br>
On Dec 24, 2010, at 7:56 , Riping WANG wrote:<br>
<br>
> In example18, for cp.x practice. I found the " ion_radius(1)<br>
> and ion_radius(2) " in the input file.<br>
> Could you please tell me something about this input parameter, and<br>
> how to set?<br>
<br>
usuallly you do not need to set it: the default value should be fine.<br>
ion_radius is the width of a gaussian distribution of charge replacing<br>
the point charge of the (pseudo-)nucleus. It should be big enough<br>
to ensure convergence of the total energy in G-space, small enough<br>
to yield negligible overlap between gaussians. Valus around 0.8 are<br>
usually fine. The total energy and forces should not change if<br>
ion_radius changes.<br>
<br>
P.<br>
---<br>
Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine<br>
via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 24 Dec 2010 15:12:19 +0530<br>
From: mohnish pandey <<a href="mailto:mohnish.iitk@gmail.com">mohnish.iitk@gmail.com</a>><br>
Subject: [Pw_forum] how does the calculation scales with number of<br>
processors<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<AANLkTimzcxdX+zRc4pHNYUQUU8Ph+qG7aiwggG=<a href="mailto:XyEnh@mail.gmail.com">XyEnh@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear QE users,<br>
I am trying to see how the runtime scales with<br>
number of processors. I did the same calculation using one node with eight<br>
processors on one cluster and 8 nodes with total 56 processors on other<br>
cluster but the time does not seem to scale linearly with the number of<br>
processors. Can anybody give me an idea how does the time scale with number<br>
of processors.<br>
Thanks a lot in advance.<br>
<br>
--<br>
Regards,<br>
MOHNISH,<br>
-----------------------------------------------------------------<br>
Mohnish Pandey<br>
Y6927262,5th Year dual degree student,<br>
Department of Chemical Engineering,<br>
IIT KANPUR, UP, INDIA<br>
-----------------------------------------------------------------<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 24 Dec 2010 11:20:34 +0100<br>
From: Stefano de Gironcoli <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>><br>
Subject: Re: [Pw_forum] how does the calculation scales with number of<br>
processors<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:4D1473F2.9090302@sissa.it">4D1473F2.9090302@sissa.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
It strongly depends on the particular calculation and on the<br>
parallelization strategy you choose. Linear scaling would be the ideal<br>
scaling which you never get.<br>
The things to keep in mind are load balancing and communication<br>
overhead. This last is affected by your communication network latency<br>
and bandwidth ... As a general rule the bigger the calculation the<br>
easier is to scale.<br>
It may be useful to have a look at the final timing summary of a<br>
calculation to see the fraction of time spent in communication (FFT<br>
scatter/gather and reduce operations) compared with the total wall clock<br>
time for your system and how this changes for different settings.<br>
Another factor to keep in mind is RAM memory as with certain<br>
parallelization strategies you can trade some speed with increased memory.<br>
<br>
stefano<br>
<br>
mohnish pandey wrote:<br>
> Dear QE users,<br>
> I am trying to see how the runtime scales with<br>
> number of processors. I did the same calculation using one node with eight<br>
> processors on one cluster and 8 nodes with total 56 processors on other<br>
> cluster but the time does not seem to scale linearly with the number of<br>
> processors. Can anybody give me an idea how does the time scale with number<br>
> of processors.<br>
> Thanks a lot in 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>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 24 Dec 2010 15:56:41 +0530<br>
From: mohnish pandey <<a href="mailto:mohnish.iitk@gmail.com">mohnish.iitk@gmail.com</a>><br>
Subject: Re: [Pw_forum] how does the calculation scales with number of<br>
processors<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:AANLkTimwTeZ2R2tGkX4ztQL6KMi3PuYop7N%2BJ1PDJZ3L@mail.gmail.com">AANLkTimwTeZ2R2tGkX4ztQL6KMi3PuYop7N+J1PDJZ3L@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thanks a lot Dr. Stefano for your reply.<br>
<br>
On Fri, Dec 24, 2010 at 3:50 PM, Stefano de Gironcoli <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>>wrote:<br>
<br>
> It strongly depends on the particular calculation and on the<br>
> parallelization strategy you choose. Linear scaling would be the ideal<br>
> scaling which you never get.<br>
> The things to keep in mind are load balancing and communication<br>
> overhead. This last is affected by your communication network latency<br>
> and bandwidth ... As a general rule the bigger the calculation the<br>
> easier is to scale.<br>
> It may be useful to have a look at the final timing summary of a<br>
> calculation to see the fraction of time spent in communication (FFT<br>
> scatter/gather and reduce operations) compared with the total wall clock<br>
> time for your system and how this changes for different settings.<br>
> Another factor to keep in mind is RAM memory as with certain<br>
> parallelization strategies you can trade some speed with increased memory.<br>
><br>
> stefano<br>
><br>
> mohnish pandey wrote:<br>
> > Dear QE users,<br>
> > I am trying to see how the runtime scales with<br>
> > number of processors. I did the same calculation using one node with<br>
> eight<br>
> > processors on one cluster and 8 nodes with total 56 processors on other<br>
> > cluster but the time does not seem to scale linearly with the number of<br>
> > processors. Can anybody give me an idea how does the time scale with<br>
> number<br>
> > of processors.<br>
> > Thanks a lot in 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>
> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
> ><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
--<br>
Regards,<br>
MOHNISH,<br>
-----------------------------------------------------------------<br>
Mohnish Pandey<br>
Y6927262,5th Year dual degree student,<br>
Department of Chemical Engineering,<br>
IIT KANPUR, UP, INDIA<br>
-----------------------------------------------------------------<br>
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------------------------------<br>
<br>
Message: 5<br>
Date: Fri, 24 Dec 2010 11:28:22 +0100<br>
From: Paolo Giannozzi <<a href="mailto:giannozz@democritos.it">giannozz@democritos.it</a>><br>
Subject: Re: [Pw_forum] how does the calculation scales with number of<br>
processors<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:E4B16AE1-0031-425C-988E-416268CBF5E0@democritos.it">E4B16AE1-0031-425C-988E-416268CBF5E0@democritos.it</a>><br>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed<br>
<br>
<br>
On Dec 24, 2010, at 10:42 , mohnish pandey wrote:<br>
<br>
> Can anybody give me an idea how does the time scale with number of<br>
> processors.<br>
<br>
please see the user guide in particular chapter 3:<br>
<a href="http://www.quantum-espresso.org/user_guide/node15.html" target="_blank">http://www.quantum-espresso.org/user_guide/node15.html</a><br>
and this, in particular the "(Too) Frequently Asked Question"<br>
<a href="http://www.fisica.uniud.it/%7Egiannozz/QE-Tutorial/" target="_blank">http://www.fisica.uniud.it/~giannozz/QE-Tutorial/</a><br>
<br>
P.<br>
---<br>
Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine<br>
via delle Scienze 208, 33100 Udine, Italy<br>
Phone +39-0432-558216, fax +39-0432-558222<br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Fri, 24 Dec 2010 20:07:29 +0800<br>
From: "jiayudai" <<a href="mailto:daijiayu@nudt.edu.cn">daijiayu@nudt.edu.cn</a>><br>
Subject: [Pw_forum] Merry Christmas<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <<a href="mailto:EMWVIYDTKKFKAFNJEUDEIMZTWAFZ.daijiayu@nudt.edu.cn">EMWVIYDTKKFKAFNJEUDEIMZTWAFZ.daijiayu@nudt.edu.cn</a>><br>
Content-Type: text/plain; charset="gb2312"<br>
<br>
Mearry Christmas to every body.<br>
<br>
Good luck for us!<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Fri, 24 Dec 2010 22:30:44 +0800<br>
From: Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>><br>
Subject: [Pw_forum] About the difference between the energy obtained<br>
from geometry optimization and single energy calculation.<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:232357947.20101224223044@yahoo.com.cn">232357947.20101224223044@yahoo.com.cn</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear PWSCF users,<br>
<br>
The geometry optimization can give the minimal energy of our system. What's the difference between the energy obtained from geometry optimization and the single energy calculation?<br>
<br>
Best regards.<br>
--<br>
Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>><br>
School of Physics and Electrical Information Science,<br>
Ningxia University, Yinchuan 750021, China<br>
GnuPG DSA: 0xD108493<br>
2010-12-24<br>
<br>
__________________________________________________<br>
¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä?<br>
<a href="http://cn.mail.yahoo.com" target="_blank">http://cn.mail.yahoo.com</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Sat, 25 Dec 2010 09:50:43 +0800<br>
From: Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>><br>
Subject: [Pw_forum] About the relationship between enthalpy and<br>
pressure.<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:1504855182.20101225095043@yahoo.com.cn">1504855182.20101225095043@yahoo.com.cn</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear PWSCF users,<br>
<br>
We all know that, the pressure-Volume, and energy--Volume curve can be obtained by fitting of EOS. But what's the relationship between enthalpy and pressure?<br>
<br>
Best regards.<br>
--<br>
Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>><br>
School of Physics and Electrical Information Science,<br>
Ningxia University, Yinchuan 750021, China<br>
GnuPG DSA: 0xD108493<br>
2010-12-25<br>
<br>
__________________________________________________<br>
¸Ï¿ì×¢²áÑÅ»¢³¬´óÈÝÁ¿Ãâ·ÑÓÊÏä?<br>
<a href="http://cn.mail.yahoo.com" target="_blank">http://cn.mail.yahoo.com</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 9<br>
Date: Sat, 25 Dec 2010 03:10:52 +0100<br>
From: Stefano de Gironcoli <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>><br>
Subject: Re: [Pw_forum] About the relationship between enthalpy and<br>
pressure.<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:4D1552AC.1090207@sissa.it">4D1552AC.1090207@sissa.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Pressure is the thermodynamical variable upon which enthalpy depends<br>
<br>
If you know E(V) you can define H(P) = min_V ( E(V) + P V )<br>
<br>
Have a look in a book of thermodynamics.<br>
<br>
stefano<br>
<br>
<br>
<br>
Hongsheng Zhao wrote:<br>
> Dear PWSCF users,<br>
><br>
> We all know that, the pressure-Volume, and energy--Volume curve can be obtained by fitting of EOS. But what's the relationship between enthalpy and pressure?<br>
><br>
> Best regards.<br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 10<br>
Date: Sat, 25 Dec 2010 09:06:09 +0530<br>
From: Prasenjit Ghosh <<a href="mailto:prasenjit.jnc@gmail.com">prasenjit.jnc@gmail.com</a>><br>
Subject: Re: [Pw_forum] About the difference between the energy<br>
obtained from geometry optimization and single energy calculation.<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<AANLkTin8_XS7tCn9KPWyYHhHCqS=<a href="mailto:Zo-oYjZpK-mjLnYW@mail.gmail.com">Zo-oYjZpK-mjLnYW@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=GB2312<br>
<br>
In geometry optimization you relax both the ionic coordinates and the<br>
electronic coordinates to obtain the minimum energy configuration. In<br>
a single energy calculation, you minimize only the electronic<br>
coordinates for a given fixed ionic position.<br>
<br>
Prasenjit<br>
<br>
On 24 December 2010 20:00, Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>> wrote:<br>
> Dear PWSCF users,<br>
><br>
> The geometry optimization can give the minimal energy of our system. What's the difference between the energy obtained from geometry optimization and the single energy calculation?<br>
><br>
> Best regards.<br>
> --<br>
> Hongsheng Zhao <<a href="mailto:zhaohscas@yahoo.com.cn">zhaohscas@yahoo.com.cn</a>><br>
> School of Physics and Electrical Information Science,<br>
> Ningxia University, Yinchuan 750021, China<br>
> GnuPG DSA: 0xD108493<br>
> 2010-12-24<br>
><br>
> __________________________________________________<br>
> ???????????????<br>
> <a href="http://cn.mail.yahoo.com" target="_blank">http://cn.mail.yahoo.com</a><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
><br>
<br>
<br>
<br>
--<br>
PRASENJIT GHOSH,<br>
Assistant Professor,<br>
IISER Pune,<br>
First floor, Central Tower, Sai Trinity Building<br>
Garware Circle, Sutarwadi, Pashan<br>
Pune, Maharashtra 411021, India<br>
<br>
Phone: +91 (20) 2590 8203<br>
Fax: +91 (20) 2589 9790<br>
<br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
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<br>
End of Pw_forum Digest, Vol 42, Issue 43<br>
****************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br><div>******************************************************************************<br>WANG Riping<br>Ph.D student, </div>
<div>Institute for Study of the Earth's Interior,Okayama University,<br>827 Yamada, Misasa, Tottori-ken 682-0193, Japan<br>Tel: +81-858-43-3739(Office), 1215(Inst)</div>
<div>E-mail: <a href="mailto:wang.riping.81@gmail.com" target="_blank">wang.riping.81@gmail.com</a><br>******************************************************************************<br><br><br></div><br>