Der prof. Paolo, Thanks very much to your reply.
1. Re: ion_radius (Paolo Giannozzi) WANG Riping 2010.12.27 On 25 December 2010 12:36, <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: ion_radius (Paolo Giannozzi) > 2. how does the calculation scales with number of processors > (mohnish pandey) > 3. Re: how does the calculation scales with number of processors > (Stefano de Gironcoli) > 4. Re: how does the calculation scales with number of processors > (mohnish pandey) > 5. Re: how does the calculation scales with number of processors > (Paolo Giannozzi) > 6. Merry Christmas (jiayudai) > 7. About the difference between the energy obtained from > geometry optimization and single energy calculation. (Hongsheng Zhao) > 8. About the relationship between enthalpy and pressure. > (Hongsheng Zhao) > 9. Re: About the relationship between enthalpy and pressure. > (Stefano de Gironcoli) > 10. Re: About the difference between the energy obtained from > geometry optimization and single energy calculation. (Prasenjit Ghosh) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Dec 2010 09:56:00 +0100 > From: Paolo Giannozzi <giannozz at democritos.it> > Subject: Re: [Pw_forum] ion_radius > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <5B32AABF-A8DA-4C29-8850-9250578A7450 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Dec 24, 2010, at 7:56 , Riping WANG wrote: > > > In example18, for cp.x practice. I found the " ion_radius(1) > > and ion_radius(2) " in the input file. > > Could you please tell me something about this input parameter, and > > how to set? > > usuallly you do not need to set it: the default value should be fine. > ion_radius is the width of a gaussian distribution of charge replacing > the point charge of the (pseudo-)nucleus. It should be big enough > to ensure convergence of the total energy in G-space, small enough > to yield negligible overlap between gaussians. Valus around 0.8 are > usually fine. The total energy and forces should not change if > ion_radius changes. > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 24 Dec 2010 15:12:19 +0530 > From: mohnish pandey <mohnish.iitk at gmail.com> > Subject: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <AANLkTimzcxdX+zRc4pHNYUQUU8Ph+qG7aiwggG=XyEnh at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear QE users, > I am trying to see how the runtime scales with > number of processors. I did the same calculation using one node with eight > processors on one cluster and 8 nodes with total 56 processors on other > cluster but the time does not seem to scale linearly with the number of > processors. Can anybody give me an idea how does the time scale with number > of processors. > Thanks a lot in advance. > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101224/094c0e6d/attachment-0001.htm > > ------------------------------ > > Message: 3 > Date: Fri, 24 Dec 2010 11:20:34 +0100 > From: Stefano de Gironcoli <degironc at sissa.it> > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4D1473F2.9090302 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > It strongly depends on the particular calculation and on the > parallelization strategy you choose. Linear scaling would be the ideal > scaling which you never get. > The things to keep in mind are load balancing and communication > overhead. This last is affected by your communication network latency > and bandwidth ... As a general rule the bigger the calculation the > easier is to scale. > It may be useful to have a look at the final timing summary of a > calculation to see the fraction of time spent in communication (FFT > scatter/gather and reduce operations) compared with the total wall clock > time for your system and how this changes for different settings. > Another factor to keep in mind is RAM memory as with certain > parallelization strategies you can trade some speed with increased memory. > > stefano > > mohnish pandey wrote: > > Dear QE users, > > I am trying to see how the runtime scales with > > number of processors. I did the same calculation using one node with > eight > > processors on one cluster and 8 nodes with total 56 processors on other > > cluster but the time does not seem to scale linearly with the number of > > processors. Can anybody give me an idea how does the time scale with > number > > of processors. > > Thanks a lot in advance. > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 24 Dec 2010 15:56:41 +0530 > From: mohnish pandey <mohnish.iitk at gmail.com> > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <AANLkTimwTeZ2R2tGkX4ztQL6KMi3PuYop7N+J1PDJZ3L at > mail.gmail.com<AANLkTimwTeZ2R2tGkX4ztQL6KMi3PuYop7N%2BJ1PDJZ3L at > mail.gmail.com> > > > Content-Type: text/plain; charset="iso-8859-1" > > Thanks a lot Dr. Stefano for your reply. > > On Fri, Dec 24, 2010 at 3:50 PM, Stefano de Gironcoli <degironc at sissa.it > >wrote: > > > It strongly depends on the particular calculation and on the > > parallelization strategy you choose. Linear scaling would be the ideal > > scaling which you never get. > > The things to keep in mind are load balancing and communication > > overhead. This last is affected by your communication network latency > > and bandwidth ... As a general rule the bigger the calculation the > > easier is to scale. > > It may be useful to have a look at the final timing summary of a > > calculation to see the fraction of time spent in communication (FFT > > scatter/gather and reduce operations) compared with the total wall clock > > time for your system and how this changes for different settings. > > Another factor to keep in mind is RAM memory as with certain > > parallelization strategies you can trade some speed with increased > memory. > > > > stefano > > > > mohnish pandey wrote: > > > Dear QE users, > > > I am trying to see how the runtime scales with > > > number of processors. I did the same calculation using one node with > > eight > > > processors on one cluster and 8 nodes with total 56 processors on other > > > cluster but the time does not seem to scale linearly with the number of > > > processors. Can anybody give me an idea how does the time scale with > > number > > > of processors. > > > Thanks a lot in advance. > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > 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 > > > > > > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > ----------------------------------------------------------------- > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101224/e6654593/attachment-0001.htm > > ------------------------------ > > Message: 5 > Date: Fri, 24 Dec 2010 11:28:22 +0100 > From: Paolo Giannozzi <giannozz at democritos.it> > Subject: Re: [Pw_forum] how does the calculation scales with number of > processors > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <E4B16AE1-0031-425C-988E-416268CBF5E0 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > > On Dec 24, 2010, at 10:42 , mohnish pandey wrote: > > > Can anybody give me an idea how does the time scale with number of > > processors. > > please see the user guide in particular chapter 3: > http://www.quantum-espresso.org/user_guide/node15.html > and this, in particular the "(Too) Frequently Asked Question" > http://www.fisica.uniud.it/~giannozz/QE-Tutorial/<http://www.fisica.uniud.it/%7Egiannozz/QE-Tutorial/> > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics, Univ. Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > ------------------------------ > > Message: 6 > Date: Fri, 24 Dec 2010 20:07:29 +0800 > From: "jiayudai" <daijiayu at nudt.edu.cn> > Subject: [Pw_forum] Merry Christmas > To: pw_forum at pwscf.org > Message-ID: <EMWVIYDTKKFKAFNJEUDEIMZTWAFZ.daijiayu at nudt.edu.cn> > Content-Type: text/plain; charset="gb2312" > > Mearry Christmas to every body. > > Good luck for us! > > > > ------------------------------ > > Message: 7 > Date: Fri, 24 Dec 2010 22:30:44 +0800 > From: Hongsheng Zhao <zhaohscas at yahoo.com.cn> > Subject: [Pw_forum] About the difference between the energy obtained > from geometry optimization and single energy calculation. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <232357947.20101224223044 at yahoo.com.cn> > Content-Type: text/plain; charset=us-ascii > > Dear PWSCF users, > > 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? > > Best regards. > -- > Hongsheng Zhao <zhaohscas at yahoo.com.cn> > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2010-12-24 > > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com > > > ------------------------------ > > Message: 8 > Date: Sat, 25 Dec 2010 09:50:43 +0800 > From: Hongsheng Zhao <zhaohscas at yahoo.com.cn> > Subject: [Pw_forum] About the relationship between enthalpy and > pressure. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <1504855182.20101225095043 at yahoo.com.cn> > Content-Type: text/plain; charset=us-ascii > > Dear PWSCF users, > > 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? > > Best regards. > -- > Hongsheng Zhao <zhaohscas at yahoo.com.cn> > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2010-12-25 > > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com > > > ------------------------------ > > Message: 9 > Date: Sat, 25 Dec 2010 03:10:52 +0100 > From: Stefano de Gironcoli <degironc at sissa.it> > Subject: Re: [Pw_forum] About the relationship between enthalpy and > pressure. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: <4D1552AC.1090207 at sissa.it> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Pressure is the thermodynamical variable upon which enthalpy depends > > If you know E(V) you can define H(P) = min_V ( E(V) + P V ) > > Have a look in a book of thermodynamics. > > stefano > > > > Hongsheng Zhao wrote: > > Dear PWSCF users, > > > > 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? > > > > Best regards. > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ------------------------------ > > Message: 10 > Date: Sat, 25 Dec 2010 09:06:09 +0530 > From: Prasenjit Ghosh <prasenjit.jnc at gmail.com> > Subject: Re: [Pw_forum] About the difference between the energy > obtained from geometry optimization and single energy calculation. > To: PWSCF Forum <pw_forum at pwscf.org> > Message-ID: > <AANLkTin8_XS7tCn9KPWyYHhHCqS=Zo-oYjZpK-mjLnYW at mail.gmail.com> > Content-Type: text/plain; charset=GB2312 > > In geometry optimization you relax both the ionic coordinates and the > electronic coordinates to obtain the minimum energy configuration. In > a single energy calculation, you minimize only the electronic > coordinates for a given fixed ionic position. > > Prasenjit > > On 24 December 2010 20:00, Hongsheng Zhao <zhaohscas at yahoo.com.cn> wrote: > > Dear PWSCF users, > > > > 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? > > > > Best regards. > > -- > > Hongsheng Zhao <zhaohscas at yahoo.com.cn> > > School of Physics and Electrical Information Science, > > Ningxia University, Yinchuan 750021, China > > GnuPG DSA: 0xD108493 > > 2010-12-24 > > > > __________________________________________________ > > ??????????????? > > http://cn.mail.yahoo.com > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > PRASENJIT GHOSH, > Assistant Professor, > IISER Pune, > First floor, Central Tower, Sai Trinity Building > Garware Circle, Sutarwadi, Pashan > Pune, Maharashtra 411021, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 42, Issue 43 > **************************************** > -- ****************************************************************************** WANG Riping Ph.D student, Institute for Study of the Earth's Interior,Okayama University, 827 Yamada, Misasa, Tottori-ken 682-0193, Japan Tel: +81-858-43-3739(Office), 1215(Inst) E-mail: wang.riping.81 at gmail.com ****************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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