[Pw_forum] radius distribution function （Pw_forum Digest, Vol 24, Issue 49）
Gabriele Sclauzero
sclauzer at sissa.it
Tue Jun 23 16:44:02 CEST 2009
I don't have the code at hand in this moment. It was not 'my' code anyway. If I remember
well I used that from Frenkel and Smit's book. You can download it from this website
http://molsim.chem.uva.nl/frenkel_smit/README.html
for instance in this case study
http://molsim.chem.uva.nl/frenkel_smit/Exercise_10/index.html
The subroutine which accumulate statistics for the radial distribution function should be
sample_gyra.f.
GS
JAY wrote:
> Dear Gabriele
>
> Thank you for your reply. I am a new learner of fortran 90, so it is
> much more helpful, if you send me your source code. I will make some
> modification where necessary. Could you please send me a copy of that
> fortran code?
>
> On Tue, Jun 23, 2009 at 6:08 PM, <pw_forum-request at pwscf.org
> <mailto:pw_forum-request at pwscf.org>> wrote:
>
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> Today's Topics:
>
> 1. Re: radius distribution function (Gabriele Sclauzero)
> 2. Re: Separating Raman modes (alexandra.carvalho at epfl.ch
> <mailto:alexandra.carvalho at epfl.ch>)
> 3. Zero of the electrostatic potential ? (Vladan Stevanovic)
> 4. Re: Zero of the electrostatic potential ? (Gabriele Sclauzero)
> 5. Re: Zero of the electrostatic potential ? (Lorenzo Paulatto)
> 6. Re: Zero of the electrostatic potential ? (Stefano de Gironcoli)
> 7. Re: Zero of the electrostatic potential ? (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Jun 2009 09:03:49 +0200
> From: Gabriele Sclauzero <sclauzer at sissa.it <mailto:sclauzer at sissa.it>>
> Subject: Re: [Pw_forum] radius distribution function
> To: PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <4A407E55.5070704 at sissa.it
> <mailto:4A407E55.5070704 at sissa.it>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Jay,
>
> JAY wrote:
> > Dear users
> >
> > Could anybody send me the fortran code for calculating radius
> > distribution function? I would like to analyze the MD results.
> Many thanks.
>
> If you meant "radial distribution function", I think you can find
> good recipes on how to
> write it on any molecular dynamics textbook, from the old classics
> by Frenkel-Smit or
> Allen-Tildesley to the modern ones. If you are really in trouble I
> can send you a fortran
> code from a course on atomistic simulations I followed at University
> (at the moment I'm
> not doing molecular dynamics calculations), but I think there are
> many people doing much
> more sophisticated things on this forum. They could help you better
> than me.
>
> GS
>
>
>
> >
> > --
> > Sincerely
> >
> > Jay
> >
> >
> > ==============================================
> > cn: Li, Jiaye
> > en: Jay Y. Lee
> >
> > M.S. in designing and developing novel materials
> >
> > Research experience:
> > *ALD precursor. ie. Metal complexes
> > *Surface modification. ie. Indium tin oxide, SiO2
> > *Gas storage and adsorption. ie. Ionic Liquids
> >
> > Skills:
> > *ab-initial method, DFT simulation and Force Field simulation
> >
> > Please contact me at:
> > 1. jameslipd at gmail.com <mailto:jameslipd at gmail.com>
> <mailto:jameslipd at gmail.com <mailto:jameslipd at gmail.com>> or
> > 2. jameslibd at gmail.com <mailto:jameslibd at gmail.com>
> <mailto:jameslibd at gmail.com <mailto:jameslibd at gmail.com>>
> >
> > ==============================================
> >
> >
> >
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it <mailto:sclauzer at sissa.it>
> |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
> o ------------------------------------------------ o
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 23 Jun 2009 10:31:06 +0200
> From: alexandra.carvalho at epfl.ch <mailto:alexandra.carvalho at epfl.ch>
> Subject: Re: [Pw_forum] Separating Raman modes
> To: PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <20090623103106.17671jzible9ehu2 at webmail.epfl.ch
> <mailto:20090623103106.17671jzible9ehu2 at webmail.epfl.ch>>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Sophia,
>
> To select which modes are Raman active you must use the selection rules.
> The following paper may be of help (see also the tables in it):
>
> Rosseau et al. Journal of Raman Spectroscopy 10, 253 (1981)
>
> If you are starting, I recommend having a look at the selection rules
> for molecules, for example in Tinkham, Group theory and Quantum
> mechanics (Dover, 1992,NY) pp248.
>
> Most likelly, you will be interested in the allowed transitions with
> highest
> frequency.
>
> Hope this helps,
>
> Alexandra
>
>
> Quoting Jonathan <sophia.nishad at gmail.com
> <mailto:sophia.nishad at gmail.com>>:
>
> > Dear users,
> >
> > I computed phonons only at the gamma point for a 64-atom binary
> > alloy. How do I separate the three main Raman modes.
> >
> > Would it be possible to get some help?
> > thanks,
> > --
> > Sophia
> > UCB, USA
> >
>
>
>
> --
>
> Alexandra Carvalho,
> Ceramics Laboratory
> Swiss Federal Institute of Technology of Lausanne (EPFL)
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Jun 2009 11:29:28 +0200
> From: Vladan Stevanovic <vladan.stevanovic at epfl.ch
> <mailto:vladan.stevanovic at epfl.ch>>
> Subject: [Pw_forum] Zero of the electrostatic potential ?
> To: pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>
> Message-ID: <4A40A078.4060305 at epfl.ch <mailto:4A40A078.4060305 at epfl.ch>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Quantum-ESPRESSO users,
>
> I am using QE for simulations of transition metal clusters. My question
> is where the code places the vacuum level in such calculations
> (nonperiodic systems in a big cell) ? To formulate differently, is it
> possible to compare directly KS eigenvalues from different
> calculations ?
>
>
> Thanks,
> Vladan Stevanovic
>
> ---------------------------------------------
> Assistant-doctorant
> EPFL SB IRRMA-GE
> PH H2 435 (B?timent PH)
> Station 3
> CH-1015 Lausanne
> tel. : +41 (0)21 693 51 08
> e-mail : vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>
> ---------------------------------------------
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Jun 2009 11:46:13 +0200
> From: Gabriele Sclauzero <sclauzer at sissa.it <mailto:sclauzer at sissa.it>>
> Subject: Re: [Pw_forum] Zero of the electrostatic potential ?
> To: PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <4A40A465.40805 at sissa.it <mailto:4A40A465.40805 at sissa.it>>
> Content-Type: text/plain; charset=iso-8859-1; format=flowed
>
>
>
> Vladan Stevanovic wrote:
> > Dear Quantum-ESPRESSO users,
> >
> > I am using QE for simulations of transition metal clusters. My
> question
> > is where the code places the vacuum level in such calculations
> > (nonperiodic systems in a big cell) ? To formulate differently, is it
>
> I think this question has been often posed and replied in the
> context of work-function
> calculation. Please first try a search on the archives using 'work
> function' or something
> similar as keys. You can also have a look to the example in
>
> examples/WorkFct_example
>
> in the QE folder.
>
> > possible to compare directly KS eigenvalues from different
> calculations ?
>
> If you want compare the distance between the eigenvalues and the
> Fermi energies in the
> respective systems, I think you can. In order to understand if you
> can compare the
> absolute (i.e. not relative to E_F) value of the eigenvalues I think
> you must first find
> the answer to your previous question.
>
>
> GS
>
>
> >
> >
> > Thanks,
> > Vladan Stevanovic
> >
> > ---------------------------------------------
> > Assistant-doctorant
> > EPFL SB IRRMA-GE
> > PH H2 435 (B?timent PH)
> > Station 3
> > CH-1015 Lausanne
> > tel. : +41 (0)21 693 51 08
> > e-mail : vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>
> > ---------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it <mailto:sclauzer at sissa.it>
> |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
> o ------------------------------------------------ o
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 23 Jun 2009 12:00:01 +0200
> From: "Lorenzo Paulatto" <paulatto at sissa.it <mailto:paulatto at sissa.it>>
> Subject: Re: [Pw_forum] Zero of the electrostatic potential ?
> To: vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>,
> "PWSCF Forum" <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <op.uvy12b18a8x26q at paulax>
> Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes
>
> In data 23 giugno 2009 alle ore 11:29:28, Vladan Stevanovic
> <vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>> ha
> scritto:
> > I am using QE for simulations of transition metal clusters. My
> question
> > is where the code places the vacuum level in such calculations
> > (nonperiodic systems in a big cell) ?
>
> Dear Vladan,
> a non-periodic system in a big periodic cell is still a periodic system!
> Hence, the integral of the potential over any possible choice of
> primitive
> cell has to be zero. This is a sufficient condition to find the zero.
>
> > To formulate differently, is it
> > possible to compare directly KS eigenvalues from different
> calculations ?
>
> In general it is NOT possible to directly compare eigenvalues of
> different
> calculations, nevertheless they can be compared taking the Fermi
> energy as
> reference.
>
> best regards
>
> --
> Lorenzo Paulatto
> SISSA & DEMOCRITOS (Trieste)
> phone: +39 040 3787 511
> skype: paulatz
> www: http://people.sissa.it/~paulatto/
>
> *** save italian brains ***
> http://saveitalianbrains.wordpress.com/
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 23 Jun 2009 12:08:03 +0200
> From: Stefano de Gironcoli <degironc at sissa.it
> <mailto:degironc at sissa.it>>
> Subject: Re: [Pw_forum] Zero of the electrostatic potential ?
> To: vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>,
> PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <4A40A983.7080108 at sissa.it
> <mailto:4A40A983.7080108 at sissa.it>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> The zero of the potential energy is the average electrostatic potential;
> as such the eigenvalues in different systems cannot be directly
> compared.
> what you need yo do is to calculate the (electrostatic) potential energy
> in the vacuum region where it should, at least for neutral systems, be
> constant and take that as the zero of the energy.
> In order to calculate the potential in the vacuum region one could adapt
> the example for the calculation of the Work Function in directory
> examples/WorkFct_example.
>
> stefano
>
> Vladan Stevanovic wrote:
> > Dear Quantum-ESPRESSO users,
> >
> > I am using QE for simulations of transition metal clusters. My
> question
> > is where the code places the vacuum level in such calculations
> > (nonperiodic systems in a big cell) ? To formulate differently, is it
> > possible to compare directly KS eigenvalues from different
> calculations ?
> >
>
> > Thanks,
> > Vladan Stevanovic
> >
> > ---------------------------------------------
> > Assistant-doctorant
> > EPFL SB IRRMA-GE
> > PH H2 435 (B?timent PH)
> > Station 3
> > CH-1015 Lausanne
> > tel. : +41 (0)21 693 51 08
> > e-mail : vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>
> > ---------------------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> ------------------------------
>
> Message: 7
> Date: Tue, 23 Jun 2009 12:07:10 +0200
> From: Paolo Giannozzi <giannozz at democritos.it
> <mailto:giannozz at democritos.it>>
> Subject: Re: [Pw_forum] Zero of the electrostatic potential ?
> To: vladan.stevanovic at epfl.ch <mailto:vladan.stevanovic at epfl.ch>,
> PWSCF Forum <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
> Message-ID: <8CD924AB-2D4E-402A-BF90-A3A392886FBB at democritos.it
> <mailto:8CD924AB-2D4E-402A-BF90-A3A392886FBB at democritos.it>>
> Content-Type: text/plain; charset="us-ascii"
>
>
> On Jun 23, 2009, at 11:29 , Vladan Stevanovic wrote:
>
> > where the code places the vacuum level in such calculations
> > (nonperiodic systems in a big cell) ? To formulate differently,
> > is it possible to compare directly KS eigenvalues from different
> > calculations ?
>
> short answer: no.
>
> V(G=0) is calculated (finite or infinite systems doesn't matter)
> as described in the attached notes. CP and PWscf have a
> different definition of V(0) so you get the same eigenvalues,
> but displaced
>
> P.
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>
>
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 24, Issue 49
> ****************************************
>
>
>
>
> --
> Sincerely
>
> Jay
>
>
> ==============================================
> cn: Li, Jiaye
> en: Jay Y. Lee
>
> M.S. in designing and developing novel materials
>
> Research experience:
> *ALD precursor. ie. Metal complexes
> *Surface modification. ie. Indium tin oxide, SiO2
> *Gas storage and adsorption. ie. Ionic Liquids
>
> Skills:
> *ab-initial method, DFT simulation and Force Field simulation
>
> Please contact me at:
> 1. jameslipd at gmail.com <mailto:jameslipd at gmail.com> or
> 2. jameslibd at gmail.com <mailto:jameslibd at gmail.com>
>
> ==============================================
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
--
o ------------------------------------------------ o
| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
| phone: +39 040 3787 511 |
| skype: gurlonotturno |
o ------------------------------------------------ o
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