[Pw_forum] External Magnetic Field
Amreen Bano
banoamreen.7 at gmail.com
Sat Mar 26 13:03:55 CET 2016
Hi everyone,
I am trying to study the effect of external electric and magnetic field on
the ferrite materials. I want to ask that, can we apply magnetic field to
the system using quantum espresso? Any suggestion will be very helpful.
Regards.
On Mar 26, 2016 4:30 PM, <pw_forum-request at pwscf.org> wrote:
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>
> Today's Topics:
>
> 1. Fiorentini-Methefessel: Surface energy (Elliot S. MENKAH)
> 2. Re: TiO2, ZO2 and BaTiO3 nanoclusters (Giuseppe Mattioli)
> 3. High symmetry Kpoint for band structure calculation for
> ibrav=-12 (Ridwan Agbaoye)
> 4. Re: Pw_forum Digest, Vol 104, Issue 21 (Vijay Khanal)
> 5. vc_relax calc. stopped converging (Vishal Gupta)
> 6. Re: Fiorentini-Methefessel: Surface energy (Ari P Seitsonen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 25 Mar 2016 12:19:18 +0000
> From: "Elliot S. MENKAH" <elliotsmenkah at yahoo.com>
> Subject: [Pw_forum] Fiorentini-Methefessel: Surface energy
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <56F52CC6.5050809 at yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Everyone,
>
> In reference to the papers *Extracting convergent surface energies from
> slab calculations, 1996,* and *Surface energies, work functions, and
> surface relaxations of low index
> metallic **surfaces from first-principles,* 2009, I'm trying to compute
> surface energies with the Fiorentini-Methefessel technique.
>
> I'm extracting the bulk energy from a linear plot of total energy vrs N.
>
> I computed the total energies of nickel surface (100) with 12, 14, 16,
> 18 and 20 atomic layers.
>
> I made a plot of total energies vrs N(Number of layers) and i got the
> equation y = 0.24897 - 171.79x
>
> With the slope being -171.79, am I right to say the bulk energy is
> -171.79Ry?
>
> Is this the right way of going about the Fiorentini-Methfessel technique?
>
> Can someone please point me in the right direction
>
> Thank you.
>
> Kind Regards,
>
> Elliot.
>
> --
> Elliot Sarpong Menkah
> Graduate Student - Computational Chemistry / Computational Material
> Science.
> Theoretical and Computational Chemistry
> Dept. of Chemistry
> Kwame Nkrumah University of Science and Technology (KNUST),
> Private Mail Bag,
> Kumasi,
> Ghana.
> Mobile:+233-243-055-717,+233-202-929-058
>
>
> Alt. Email: esmenkah at knust.edu.gh
> elliotsmenkah at gmail.com
> elliotsmenkah at hotmail.com
>
> webpage: http://chemistry.knust.edu.gh/MMC/group-members/ESMenkah
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 25 Mar 2016 14:00:52 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Subject: Re: [Pw_forum] TiO2, ZO2 and BaTiO3 nanoclusters
> To: pw_forum at pwscf.org
> Message-ID: <5592743.pJqNtu1jHW at amore2>
> Content-Type: text/plain; charset="ISO-8859-1"
>
>
> Dear Andrey
> Sorry for the late reply.
>
> > I read the manual. So, need I take the parameters assume_isolated?
>
> Yes, the Makov-Payne implementation of assume_isolated, e.g., provides
> decoupling of long-range electrostatic interaction between periodically
> replicated images of your clusters, as well as an estimate of the vacuum
> level, useful to the "absolute" alignment of band edges of different
> materials. It also works fine with the ENVIRON plug-in; if you are
> planning to perform calculations of charged clusters you may want to flick
> through
> the environ homepage here:
>
> http://www.quantum-environment.org/
>
> > I read the manual. So, need I take the parameters lda_plus_u?
>
> Yes, but you should know what you are doing... Read carefully the DFT+U
> review papers, specially this one:
>
> Himmetoglu et al International Journal of Quantum Chemistry 2014, 114, 14
>
> For an interesting discussion about some limits of the simplified DFT+U
> approach in the case of TiO2 and ZnO you may flick through this paper:
>
> Agapito et al Phys. Rev. X 5, 011006 2015
>
> and for a "semiempirical" estimate of U in the cases of TiO2 and ZnO you
> may read my papers (for ZnO also the SuppInfo):
>
> J. Phys. Chem. C 2012, 116, 15439
> J. Phys. Chem. C 2014, 118, 29928
>
> HTH
> Giuseppe
>
> On Wednesday, March 23, 2016 12:23:22 PM Andrey Chibisov wrote:
> > Dear Colleagues!
> > I have some questions.
> > I want to calculate the electronic structure of the TiO2, ZO2 and BaTiO3
> nanoclusters and get good value of bandgap.
> > I read the manual. So, need I take the parameters assume_isolated and
> lda_plus_u?
> >
> > --
> > Best regards,
> > Andrey Chibisov. Ph.D.
> > Numerical method of mathematical physics Laboratory,
> > Computational Center, Russian Academy of Sciences.
> > Khabarovsk, Russia
> > Web page: https://www.researchgate.net/profile/A_Chibisov
> > http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en
>
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> v. Salaria Km 29,300 - C.P. 10
> I 00015 - Monterotondo Stazione (RM), Italy
> Tel + 39 06 90672836 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
> http://www.ism.cnr.it/english/staff/mattiolig
> ResearcherID: F-6308-2012
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 25 Mar 2016 21:43:13 +0000 (UTC)
> From: Ridwan Agbaoye <agbaoyeridwan at yahoo.com>
> Subject: [Pw_forum] High symmetry Kpoint for band structure
> calculation for ibrav=-12
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <1440269663.909740.1458942193369.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Good day all
> I appreciate the forum support all this while, i am grateful
>
> I have been working on a molecular crystal for a while, now i am at the
> stage of plotting the band structure. please i need to be guided on how to
> determine my high symmetry kpoint required for band structure plot for a
> monoclinic system with ibrav=-12 .?
> I will appreciate if i can get literatures that can guide me on how to
> determine the high symmetry point
> Agbaoye, Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc(in
> view)
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> ------------------------------
>
> Message: 4
> Date: Fri, 25 Mar 2016 20:30:09 -0700
> From: Vijay Khanal <vj.khanal20 at gmail.com>
> Subject: Re: [Pw_forum] Pw_forum Digest, Vol 104, Issue 21
> To: pw_forum <pw_forum at pwscf.org>
> Message-ID:
> <CAJ+hQ2c6mETzAgszK0VPEk=VEMm6wvk8u3-hn=
> veMzoRogQJCA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE users,
>
> Being a novice user, I am not entirely sure why would we like to do
> *nscf *calculations
> even if we have *scf *and *relax* calculations. Looks like we need nscf for
> post-processing of Bandstructure calculations, but there should definitely
> be more genuine reasons for doing that, I believe. Could you please clarify
> it for me?
>
> Thank you.
>
> Respectfully,
> Vijay Khanal.
>
>
>
> *Vijay Khanal*
> Department of Physics
> University of Nevada, Reno
> Phone:(1-*775-440-7036)*
>
>
> On Wed, Mar 23, 2016 at 4:00 AM, <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://pwscf.org/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: The format of potential file in example Al100
> > workfunction (Giovanni Cantele)
> > 2. citing PSLibrary (Merlin Meheut)
> > 3. Re: citing PSLibrary (Giuseppe Mattioli)
> > 4. Re: negative occupations in DFT+U for nonmagnetic
> > semiconductor (Mostafa Youssef)
> > 5. Re: Specifying initial velocities in MD (Ilya Ryabinkin)
> > 6. General question on restarted calculation (Cameron Foss)
> > 7. vc_relax calc. stopped converging (Vishal Gupta)
> > 8. TiO2, ZO2 and BaTiO3 nanoclusters (Andrey Chibisov)
> > 9. RE : Regarding PDOS (efi dwi indari)
> > 10. Band Diagram: Regarding (Suresh A)
> > 11. xmgrace installation problem (Vijay Khanal)
> > 12. Re: xmgrace installation problem (Mike Atambo)
> > 13. Re: xmgrace installation problem (Giovanni Cantele)
> > 14. Re: Band Diagram: Regarding (Giovanni Cantele)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 22 Mar 2016 12:37:04 +0100
> > From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> > Subject: Re: [Pw_forum] The format of potential file in example Al100
> > workfunction
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID: <26AEF445-16EF-4CA1-B471-2F5AA4AEC056 at spin.cnr.it>
> > Content-Type: text/plain; charset="utf-8"
> >
> > L3:
> > WRITE (iunplot, '(3f20.10,i6)') gcutm, dual, ecutwfc
> >
> > ecutwfc = input variable, kinetic energy cutoff (Ry) for wave functions
> >
> > dual = ecutrho/ecutwfc, where ecutrho=kinetic energy cutoff (Ry) for
> > charge density and potential
> >
> > by default dual=4, this can be easily obtained by representing the charge
> > density in terms of the Fourier expansions of the Kohn-Sham orbitals,
> > dual should be set >4 only if not norm conserving pseudo potentials are
> > used in the calculation
> >
> >
> > gcutm : ecutrho/(2 pi/a)^2, cut-off for |G|^2
> >
> >
> > L4:
> > WRITE (iunplot, '(i4,3x,a2,3x,f5.2)') &
> > (nt, atm (nt), zv (nt), nt=1, ntyp)
> >
> > so, in your case, atomic species nt=1 has symbol atm(nt)=Al with valence
> > zv(nt)=3 because the pseudo you use to represent that atom (Al) is built
> > using three electrons in the valence
> >
> > Giovanni
> >
> >
> >
> > > On 22 Mar 2016, at 03:50, Yue-Wen Fang <yuewen.fang at gmail.com> wrote:
> > >
> > > Dear Prof. Giovanni,
> > >
> > > Thanks for your answer. I read it and average.f90, but still don't know
> > the specific meaning of L3 and 3.00 in L4. Could you help explain them?
> > >
> > > Thanks for your time.
> > >
> > >
> > > L1: 18 18 120 18 18 120 4 1
> > > L2: 6 5.42350901 0.00000000 6.36396103
> > 0.00000000 0.00000000 0.00000000
> > > L3: 74.5076722547(gcutm) 4.0000000000(dual)
> > 25.000000000(ecuwfc) 11
> > > L4: 1 Al 3.00(zv?)
> > > L5: 1 0.000000000 0.000000000 4.242640687 1
> > > L6: 2 0.500000000 0.500000000 3.535533906 1
> > > L7: 3 0.000000000 0.000000000 2.828427125 1
> > > L8: 4 0.500000000 0.500000000 2.121320344 1
> > >
> > > Bests
> > > Fang
> > >
> > > 2016-03-15 18:42 GMT+08:00 Giovanni Cantele <
> > giovanni.cantele at spin.cnr.it <mailto:giovanni.cantele at spin.cnr.it>>:
> > > see PP/src/write_io_header.f90
> > >
> > > Giovanni
> > >
> > >> On 15 Mar 2016, at 09:05, Yue-Wen Fang <yuewen.fang at gmail.com
> <mailto:
> > yuewen.fang at gmail.com>> wrote:
> > >>
> > >> Dear users,
> > >>
> > >> In the example of the workfunction for Al(100), we can get a file
> > "Al100.pot" after executing pp.x after runing pp.x
> > >>
> > >> The header part in the file is shown below (L1, L2... denote the line
> > numbers):
> > >>
> > >> L1: 18 18 120 18 18 120 4 1
> > >> L2: 6 5.42350901 0.00000000 6.36396103
> > 0.00000000 0.00000000 0.00000000
> > >> L3: 74.5076722547 4.0000000000 25.0000000000 11
> > >> L4: 1 Al 3.00
> > >> L5: 1 0.000000000 0.000000000 4.242640687 1
> > >> L6: 2 0.500000000 0.500000000 3.535533906 1
> > >> L7: 3 0.000000000 0.000000000 2.828427125 1
> > >> L8: 4 0.500000000 0.500000000 2.121320344 1
> > >>
> > >> Could anyone explain the meaning of this part? I didn't find the code
> > in pwscf which generates the header part.
> > >>
> > >> Actually I can guess some of them like FFT grid and coordinates, but
> > I'm not sure for each number shown above. I appreciate experienced users'
> > giving a hand. Many thanks.
> > >>
> > >> Bests
> > >> Fang
> > >> --
> > >>
> >
> ------------------------------------------------------------------------------------------------------------
> > >> Yue-Wen FANG, PhD candidate
> > >> East China Normal University? <http://english.ecnu.edu.cn/>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Pw_forum mailing list
> > >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > >> http://pwscf.org/mailman/listinfo/pw_forum <
> > http://pwscf.org/mailman/listinfo/pw_forum>
> > > --
> > >
> > > Giovanni Cantele, PhD
> > > CNR-SPIN
> > > c/o Dipartimento di Fisica
> > > Universita' di Napoli "Federico II"
> > > Complesso Universitario M. S. Angelo - Ed. 6
> > > Via Cintia, I-80126, Napoli, Italy
> > > e-mail: giovanni.cantele at spin.cnr.it <mailto:
> > giovanni.cantele at spin.cnr.it>
> > > Phone: +39 081 676910
> > > Skype contact: giocan74
> > >
> > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 <
> > http://www.researcherid.com/rid/A-1951-2009>
> > > Web page: http://people.na.infn.it/~cantele <
> > http://people.na.infn.it/~cantele>
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> > > http://pwscf.org/mailman/listinfo/pw_forum <
> > http://pwscf.org/mailman/listinfo/pw_forum>
> > >
> > >
> > >
> > > --
> > >
> >
> ------------------------------------------------------------------------------------------------------------
> > > Yue-Wen FANG, PhD candidate
> > > East China Normal University? <http://english.ecnu.edu.cn/>
> > >
> > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > --
> >
> > Giovanni Cantele, PhD
> > CNR-SPIN
> > c/o Dipartimento di Fisica
> > Universita' di Napoli "Federico II"
> > Complesso Universitario M. S. Angelo - Ed. 6
> > Via Cintia, I-80126, Napoli, Italy
> > e-mail: giovanni.cantele at spin.cnr.it
> > Phone: +39 081 676910
> > Skype contact: giocan74
> >
> > ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> > Web page: http://people.na.infn.it/~cantele
> >
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> >
> > ------------------------------
> >
> > Message: 2
> > Date: Tue, 22 Mar 2016 12:23:34 +0000
> > From: Merlin Meheut <merlin.meheut at gmail.com>
> > Subject: [Pw_forum] citing PSLibrary
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <
> > CAOZRYoC2-NTt63LKbjCwf5BzUoqVqs0PxLoLod7P4QdkA+1pJg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear PWSCF users,
> >
> > I have made important use of some pseudopotentials present in the
> > PSLibrary, and I would like to describe them in a publication. More
> > precisely, I used the pseudopotentials Mg.blyp-spn-rrkjus_psl.1.0.0.UPF,
> > K.blyp-spn-rrkjus_psl.1.0.0.UPF, and Li.blyp-sl-rrkjus_psl.1.0.0.UPF.
> >
> > Do you have any advice on how to describe them, and/or on how to cite the
> > PSLIbrary (version 1.0.0)?
> >
> > Thank you very much for any advice,
> >
> > Best regards,
> >
> > Merlin Meheut
> >
> > --
> > Merlin M?heut
> > adresse labo:
> > GET - OMP - Universit? Paul Sabatier
> > 14 avenue Edouard Belin
> > 31400 Toulouse
> > FRANCE
> > tel: (+33) 5 61 33 26 17
> > -------------- next part --------------
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> >
> > ------------------------------
> >
> > Message: 3
> > Date: Tue, 22 Mar 2016 13:49:05 +0100
> > From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> > Subject: Re: [Pw_forum] citing PSLibrary
> > To: pw_forum at pwscf.org
> > Message-ID: <4817076.5OUG813eSe at amore2>
> > Content-Type: text/plain; charset="utf-8"
> >
> >
> > Dear Merlin
> >
> > Dal Corso, A. Comput. Mater. Sci. 2014, 95, 337?350.
> >
> > HTH
> > Giuseppe
> >
> > On Tuesday, March 22, 2016 12:23:34 PM Merlin Meheut wrote:
> > > Dear PWSCF users,
> > >
> > > I have made important use of some pseudopotentials present in the
> > > PSLibrary, and I would like to describe them in a publication. More
> > > precisely, I used the pseudopotentials
> Mg.blyp-spn-rrkjus_psl.1.0.0.UPF,
> > > K.blyp-spn-rrkjus_psl.1.0.0.UPF, and Li.blyp-sl-rrkjus_psl.1.0.0.UPF.
> > >
> > > Do you have any advice on how to describe them, and/or on how to cite
> the
> > > PSLIbrary (version 1.0.0)?
> > >
> > > Thank you very much for any advice,
> > >
> > > Best regards,
> > >
> > > Merlin Meheut
> >
> > ********************************************************
> > - Article premier - Les hommes naissent et demeurent
> > libres et ?gaux en droits. Les distinctions sociales
> > ne peuvent ?tre fond?es que sur l'utilit? commune
> > - Article 2 - Le but de toute association politique
> > est la conservation des droits naturels et
> > imprescriptibles de l'homme. Ces droits sont la libert?,
> > la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> > ********************************************************
> >
> > Giuseppe Mattioli
> > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> > v. Salaria Km 29,300 - C.P. 10
> > I 00015 - Monterotondo Stazione (RM), Italy
> > Tel + 39 06 90672836 - Fax +39 06 90672316
> > E-mail: <giuseppe.mattioli at ism.cnr.it>
> > http://www.ism.cnr.it/english/staff/mattiolig
> > ResearcherID: F-6308-2012
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Tue, 22 Mar 2016 14:28:37 +0000
> > From: Mostafa Youssef <myoussef at mit.edu>
> > Subject: Re: [Pw_forum] negative occupations in DFT+U for nonmagnetic
> > semiconductor
> > To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> > Message-ID:
> > <
> > 0AE34FFC1339F64387D182A8D7E4D99B6D18A9DB at OC11EXPO32.exchange.mit.edu>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you for the clarification, Prof. de Gironcoli. I think I
> > misinterpreted the meaning of the matrix elements.
> >
> > Best Regards,
> > Mostafa
> > -------------- next part --------------
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> >
> > ------------------------------
> >
> > Message: 5
> > Date: Tue, 22 Mar 2016 10:30:44 -0400
> > From: Ilya Ryabinkin <igryabinkin at gmail.com>
> > Subject: Re: [Pw_forum] Specifying initial velocities in MD
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID:
> > <CAHcT10qrp7Et0KTgeKUjh7nZYN=
> > SJ7pRqg7j0PD9zvmRv3GRXA at mail.gmail.com>
> > Content-Type: text/plain; charset=UTF-8
> >
> > Well, I figured it out by myself... Here is a short tutorial for those
> > who might be interested.
> >
> > All below is pertinent to QE 5.2.1.
> > There is an undocumented feature allowing one to specify initial
> > velocities.
> >
> > 1. Add to the input list
> > &IONS
> > ion_velocities = 'from_input'
> > /
> >
> > 2. Add a new input card "ATOMIC_VELOCITIES".
> >
> > Here is the quotation from the source code (read_card_f90):
> > ! ATOMIC_VELOCITIES
> > !
> > ! read velocities (in atomic units) from standard input
> > !
> > ! Syntax:
> > !
> > ! ATOMIC_VELOCITIES
> > ! label(1) Vx(1) Vy(1) Vz(1)
> > ! ....
> > ! label(n) Vx(n) Vy(n) Vz(n)
> > !
> > ! Example:
> > !
> > ! ???
> > !
> > ! Where:
> > !
> > ! label (character(len=4)) atomic label
> > ! Vx(:), Vy(:) and Vz(:) (REAL) x, y and z velocity components of
> > ! the ions
> > !
> >
> >
> > Two caveats:
> > Caveat #1. Velocities are given in bohr/1Rut, not in atomic units as
> > the source says!
> >
> > Caveat #2. If there are no frozen atoms in a cell, the center-of-mass
> > velocity will be subtracted from
> > the given velocities leading to a different value of the initial
> > kinetic energy. If any of atomic coordinate is
> > frozen, the velocities are assigned as given.
> >
> >
> > --
> > *******************************************************
> > Ilya Ryabinkin
> > Postdoctoral Scholar
> > Physical and Environmental Sciences
> > University of Toronto Scarborough
> > http://www.utsc.utoronto.ca/~aizmaylov/Members.html
> > *******************************************************
> >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Tue, 22 Mar 2016 16:29:20 -0400
> > From: Cameron Foss <cjfoss at umass.edu>
> > Subject: [Pw_forum] General question on restarted calculation
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <CANUcA0PcWSystyeUB0RqfUD=b=
> > 1xqTcB1j1mNk5fBRJvpkc72g at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I have had mixed results with restarted calculations when calculating
> > phonons in TMD MoSe2. Particularly, a dispersion obtained from an
> > interrupted simulation that was restarted (after an unplanned stop)
> > returned an 'ok' dispersion despite having some negative frequencies in
> the
> > ZA branch (the ZA being the characteristic quadratic flexural phonon mode
> > in 2D materials). This 'ok' dispersion was calculated on a 6x6x4 MP grid
> > size. In an attempt to refine the simulation and avoid numerical errors,
> I
> > increased the MP grid size to 17x17x1 (in literature a 2D grid size
> > definition has been used to generate the dispersion of other 2D materials
> > like MoS2) and implemented controlled stops within walltime limits to
> avoid
> > unplanned interruptions in the simulation. Another change between the old
> > and new simulation was the fact that I isolated the monolayer in the
> middle
> > of the unit cell rather than resting at the bottom (I have provided both
> > input scripts). The dispersion obtained from this latter simulation was
> > practically nonsense as if the input file defined a highly unstable
> > structure despite the convergence of relaxation calculations. In short
> the
> > first interrupted simulation on a more coarse MP grid yield far better
> > results than the isolated denser grid simulation. Is there any insight as
> > to what possible errors that may have occurred? or is it possible that I
> > did not trace the BZ appropriately as a result of the height offset? (I
> did
> > attempt to trace along the z-direction at the Gamma and K points and
> their
> > values were accurate and invariant of z despite the rest of the
> dispersion
> > being completely incorrect)
> >
> > %% the first input file that gave an ok dispersion %%
> > Phonons in MoSe2
> > &control
> > calculation='scf'
> > restart_mode='from_scratch',
> > !pseudo_dir='directory where pseudopotentials are stored/',
> > !outdir='directory where large files are written/'
> > pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',
> > outdir='/oasis/scratch/cjfoss/temp_project/out'
> > prefix='mose2PH',
> > /
> > &system
> > ibrav=4, celldm(1)=6.2134195, celldm(3)=8,
> > nat=3, ntyp=2, ecutwfc =140
> > /
> > &electrons
> > conv_thr = 1.0d-14
> > mixing_beta = 0.7
> > /
> > ATOMIC_SPECIES
> > Mo 95.94 Mo.pw-mt_fhi.UPF
> > Se 78.96 Se.pw-mt_fhi.UPF
> > ATOMIC_POSITIONS alat
> > Se 0.000000000 0.000000000 0.000000000
> > Mo 0.500000000 0.288675135 0.493465193
> > Se 0.000000000 0.000000000 0.986930347
> > K_POINTS automatic
> > 6 6 4 1 1 1
> >
> >
> > %% the second input file that gave bad results %%
> > Phonons in MoSe2
> > &control
> > calculation='scf'
> > restart_mode='from_scratch',
> > !pseudo_dir='directory where pseudopotentials are stored/',
> > !outdir='directory where large files are written/'
> > pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',
> > outdir='/home/cjfoss/espresso-5.1/2dout'
> > prefix='mose2PH_v7',
> > /
> > &system
> > ibrav=4, celldm(1)=6.2134195, celldm(3)=8,
> > nat=3, ntyp=2, ecutwfc =140
> > /
> > &electrons
> > conv_thr = 1.0d-12
> > mixing_beta = 0.7
> > /
> > ATOMIC_SPECIES
> > Mo 95.94 Mo.pw-mt_fhi.UPF
> > Se 78.96 Se.pw-mt_fhi.UPF
> > ATOMIC_POSITIONS alat
> > Se 0.000000000 0.000000000 3.000000000
> > Mo 0.500000000 0.288675135 3.493465193
> > Se 0.000000000 0.000000000 3.986930347
> > K_POINTS automatic
> > 17 17 1 1 1 1
> >
> > %% note the main differences are the MP grid size and the z-direction
> > offset.
> >
> > Any insight is welcome!
> >
> > Best regards,
> > Cameron
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160322/39b0e2a9/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Wed, 23 Mar 2016 07:16:33 +0530
> > From: Vishal Gupta <vishal.gupta at iitrpr.ac.in>
> > Subject: [Pw_forum] vc_relax calc. stopped converging
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID:
> > <CANAZiL-+ZKJGtUfG-+mhqGQ2EO3rUVpsjfzQGGs=
> > HndFEeaGXw at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi all,
> > I've been running a vc_relax calculation on a 40 atom system. The
> > calculation worked fine for some cycles. The total force had come down to
> > 0.108 and when the no of cycles was complete, I started another
> calculation
> > with the final atomic positions and lattice parametres.
> > In this new file, the force started increasing and it increased to 0.2
> and
> > now the iterations don't converge even in 400 steps.
> > The CELL parameters are :-
> > [&Ions/]
> > /
> > &CELL
> > cell_dynamics= 'damp-w' ,
> > cell_dofree='xy' ,
> > /
> >
> > Please tell me where am I making the mistake.
> > Thank You.
> > Best Regards,
> > Vishal Gupta
> >
> > B.Tech. 3rd year Mechanical
> > Indian Institute of Technology Ropar
> > Rupnagar (140001), Punjab, India.
> > Email :- vishal.gupta at iitrpr.ac.in
> > RMML, IIT Ropar
> > <
> >
> https://sites.google.com/a/iitrpr.ac.in/ropar-mechanics-of-materials-laboratory/people
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/f5c1d98a/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Wed, 23 Mar 2016 12:23:22 +1000
> > From: Andrey Chibisov <andreichibisov at yandex.ru>
> > Subject: [Pw_forum] TiO2, ZO2 and BaTiO3 nanoclusters
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID: <1844551458699802 at web27g.yandex.ru>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/2d121742/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Wed, 23 Mar 2016 10:03:34 +0700
> > From: efi dwi indari <efidwiindari at gmail.com>
> > Subject: [Pw_forum] RE : Regarding PDOS
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <CAHN8SfnTEAdbwTsO28xSKsQJryGirtgDjO0qzs_8uccmhdgG=
> > g at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Mr. Sushant Kumar Behera,
> >
> > I use gnuplot. There is a nice tutorial at this following link :
> > http://people.duke.edu/~hpgavin/gnuplot.html
> >
> > Hope it helps.
> >
> > Best Regards,
> >
> > Efi Dwi Indari
> > Research Assistant Institut Teknologi Bandung
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/b7be6450/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Wed, 23 Mar 2016 10:03:39 +0530
> > From: Suresh A <suresh2007pgp19 at gmail.com>
> > Subject: [Pw_forum] Band Diagram: Regarding
> > To: pw_forum at pwscf.org
> > Message-ID:
> > <
> > CAE_UR+WMxfq7eH0g+SWy5wi08_fYa1iDhKCK-eZud_qnKOkSYQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear All,
> > Band structure is plotted using plotband.x executable in
> > espresso. Can one use plotband.x to do other things like colouring band
> > structures, differentiating specific band with different colour and
> making
> > journal publication quality pictures?. If there is other software please
> > direct me towards it.
> > Thanks in advance
> > With Regards,
> > A.Suresh,
> > Research Scholar,
> > Madurai Kamaraj University,
> > Madurai.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/47ded011/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 11
> > Date: Tue, 22 Mar 2016 21:49:40 -0700
> > From: Vijay Khanal <vj.khanal20 at gmail.com>
> > Subject: [Pw_forum] xmgrace installation problem
> > To: pw_forum <pw_forum at pwscf.org>
> > Message-ID:
> > <CAJ+hQ2cOPmJG5jhVdtRaJo8Gik3MEMSnTtEZ7H=
> > Xup85jK5sVQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear everyone,
> >
> > I am a novice user of Quantum Espresso. I have been facing the following
> > issue since the day I had tried to visualize the bandstructure of
> Silicon.
> >
> > I was trying to install xmgrace in my mac OSX Yosemite(10.10.5).
> Following
> > the installation steps, looks like the dependency(MOTIF) is not
> installed.
> > I tired installing it from
> >
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg
> > ,
> > it actually is installed; but then when I get back to xmgrace
> installation,
> > it says "configure: error: M*tif has not been found". I tried with its
> > source too (
> >
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz
> > ),
> > but couldn't do it. Please let me know how I can get rid of this issue.
> >
> > If there exists any easier alternative to xmgrace, that would be even
> > better.
> >
> > Thank you so much for your time!
> >
> >
> > Sincerely,
> > Vijay Khanal
> > *Vijay Khanal*
> > Department of Physics
> > University of Nevada, Reno
> > Phone:(1-*775-440-7036)*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160322/a90be4a0/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 12
> > Date: Wed, 23 Mar 2016 09:17:31 +0000
> > From: Mike Atambo <mikeat4999 at gmail.com>
> > Subject: Re: [Pw_forum] xmgrace installation problem
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID:
> > <CAEBLkK-LeNT1=
> > mbFG8FifbkXLskJZ4YraQg5du1-LyuYODtTzQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Vijay,
> > You may want to give more details (like the error when installing Motif)
> > this will help other Mac users to spot your particular error,
> > but, that said iv heard of something called brew for MAC users, try it,
> > here are some instructions on stackoverflow:
> > http://stackoverflow.com/a/28999461/1908184
> >
> > On Wed, Mar 23, 2016 at 5:50 AM Vijay Khanal <vj.khanal20 at gmail.com>
> > wrote:
> >
> > > Dear everyone,
> > >
> > > I am a novice user of Quantum Espresso. I have been facing the
> following
> > > issue since the day I had tried to visualize the bandstructure of
> > Silicon.
> > >
> > > I was trying to install xmgrace in my mac OSX Yosemite(10.10.5).
> > Following
> > > the installation steps, looks like the dependency(MOTIF) is not
> > installed.
> > > I tired installing it from
> > >
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg
> > ,
> > > it actually is installed; but then when I get back to xmgrace
> > installation,
> > > it says "configure: error: M*tif has not been found". I tried with its
> > > source too (
> > >
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz
> > ),
> > > but couldn't do it. Please let me know how I can get rid of this issue.
> > >
> > > If there exists any easier alternative to xmgrace, that would be even
> > > better.
> > >
> > > Thank you so much for your time!
> > >
> > >
> > > Sincerely,
> > > Vijay Khanal
> > > *Vijay Khanal*
> > > Department of Physics
> > > University of Nevada, Reno
> > > Phone:(1-*775-440-7036)*
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/74e6cc4b/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 13
> > Date: Wed, 23 Mar 2016 10:34:16 +0100
> > From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> > Subject: Re: [Pw_forum] xmgrace installation problem
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID: <BA659F88-736C-4AEB-A660-50C74AC8187D at spin.cnr.it>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > you can use gnu plot but else xmgrace.
> >
> > For Mac Os X the most straightforward way to install those packages in
> > through macports, see instruction at
> > https://www.macports.org <https://www.macports.org/>
> > on how to install MacPOrts and, then, external packages.
> >
> > Giovanni
> >
> >
> > > On 23 Mar 2016, at 05:49, Vijay Khanal <vj.khanal20 at gmail.com> wrote:
> > >
> > > Dear everyone,
> > >
> > > I am a novice user of Quantum Espresso. I have been facing the
> following
> > issue since the day I had tried to visualize the bandstructure of
> Silicon.
> > >
> > > I was trying to install xmgrace in my mac OSX Yosemite(10.10.5).
> > Following the installation steps, looks like the dependency(MOTIF) is not
> > installed. I tired installing it from
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg
> > <
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg
> >,
> > it actually is installed; but then when I get back to xmgrace
> installation,
> > it says "configure: error: M*tif has not been found". I tried with its
> > source too (
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz
> > <
> >
> http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz
> >),
> > but couldn't do it. Please let me know how I can get rid of this issue.
> > >
> > > If there exists any easier alternative to xmgrace, that would be even
> > better.
> > >
> > > Thank you so much for your time!
> > >
> > >
> > > Sincerely,
> > > Vijay Khanal
> > > Vijay Khanal
> > > Department of Physics
> > > University of Nevada, Reno
> > > Phone:(1-775-440-7036)
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > --
> >
> > Giovanni Cantele, PhD
> > CNR-SPIN
> > c/o Dipartimento di Fisica
> > Universita' di Napoli "Federico II"
> > Complesso Universitario M. S. Angelo - Ed. 6
> > Via Cintia, I-80126, Napoli, Italy
> > e-mail: giovanni.cantele at spin.cnr.it
> > Phone: +39 081 676910
> > Skype contact: giocan74
> >
> > ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> > Web page: http://people.na.infn.it/~cantele
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/135507e4/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 14
> > Date: Wed, 23 Mar 2016 10:36:59 +0100
> > From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> > Subject: Re: [Pw_forum] Band Diagram: Regarding
> > To: PWSCF Forum <pw_forum at pwscf.org>
> > Message-ID: <CA65D738-231A-4608-9182-814733D4E715 at spin.cnr.it>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > any software able to plot data files, like gnu plot, xmgrace, etc. is
> > suitable for plotting high quality pictures, under Linux/MacOsX
> > environments.
> >
> > Giovanni
> >
> >
> > > On 23 Mar 2016, at 05:33, Suresh A <suresh2007pgp19 at gmail.com> wrote:
> > >
> > > Dear All,
> > > Band structure is plotted using plotband.x executable in
> > espresso. Can one use plotband.x to do other things like colouring band
> > structures, differentiating specific band with different colour and
> making
> > journal publication quality pictures?. If there is other software please
> > direct me towards it.
> > > Thanks in advance
> > > With Regards,
> > > A.Suresh,
> > > Research Scholar,
> > > Madurai Kamaraj University,
> > > Madurai.
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > --
> >
> > Giovanni Cantele, PhD
> > CNR-SPIN
> > c/o Dipartimento di Fisica
> > Universita' di Napoli "Federico II"
> > Complesso Universitario M. S. Angelo - Ed. 6
> > Via Cintia, I-80126, Napoli, Italy
> > e-mail: giovanni.cantele at spin.cnr.it
> > Phone: +39 081 676910
> > Skype contact: giocan74
> >
> > ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> > Web page: http://people.na.infn.it/~cantele
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://pwscf.org/pipermail/pw_forum/attachments/20160323/00008f29/attachment-0001.html
> >
> > ------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > End of Pw_forum Digest, Vol 104, Issue 21
> > *****************************************
> >
> -------------- next part --------------
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> ------------------------------
>
> Message: 5
> Date: Sat, 26 Mar 2016 10:35:36 +0530
> From: Vishal Gupta <vishal.gupta at iitrpr.ac.in>
> Subject: [Pw_forum] vc_relax calc. stopped converging
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <
> CANAZiL_gwz0RKY_FfqWQgpfZ1W-Nx_1M9FSdkj0aH+irnXP0+A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
> I've been running a vc_relax calculation on a 40 atom system. The
> calculation worked fine for some cycles. The total force had come down to
> 0.108. After some time. the force started increasing and it increased to
> 0.2 and now the iterations don't converge even in 400 steps.
> The CELL parameters are :-
> [&Ions/]
> /
> &CELL
> cell_dynamics= 'damp-w' ,
> cell_dofree='xy' ,
> /
> P.S. Ive tried doing it with 'damp-pr' also but the same problem persists.
> Please tell me where am I making the mistake.
> Thank You.
> Best Regards,
> Vishal Gupta
>
> B.Tech. 3rd year Mechanical
> Indian Institute of Technology Ropar
> Rupnagar (140001), Punjab, India.
> Email :- vishal.gupta at iitrpr.ac.in
> RMML, IIT Ropar
> <
> https://sites.google.com/a/iitrpr.ac.in/ropar-mechanics-of-materials-laboratory/people
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 6
> Date: Sat, 26 Mar 2016 10:21:28 +0100 (CET)
> From: Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>
> Subject: Re: [Pw_forum] Fiorentini-Methefessel: Surface energy
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <alpine.DEB.2.10.1603261013310.11281 at wigner.ens.fr>
> Content-Type: text/plain; charset="utf-8"
>
>
> Dear Elliot,
>
> I am not sure if I understood correctly your description, but basically:
> You plot the energy per layer as a function of the inverse of number of
> layers, so starting from the definition
>
> E_surf = [ E_slab(N) - N * E_bulk ] / ( 2 A ) ,
>
> where
>
> Esurf = surface energy per unit area A - sometimes one plots the surface
> energy per unit cell; 2 because the slab has two surfaces,
>
> E_slab(N) = total energy of the slab of N layers
>
> E_bulk = the "unknown" bulk energy
>
> Rewriting ? la Fiorentini et Methfessel,
>
> E_slab(N)/N = 2A (1/N) E_surf + E_bulk
>
> which is equivalent of an equation
>
> y = 2A E_surf x + E_bulk ^= a x + b
>
> where E_surf and E_bulk are the unknowns, obtained from the fit. So how do
> you find E_bulk from this equation (hint: What happens when N ->
> infinity?)? And what does the slope yield?
>
> Greetings from Paris,
>
> apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
> Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Sup?rieure (ENS), D?partement de Chimie, Paris
> Mobile (F) : +33 789 37 24 25 (CH) : +41 79 71 90 935
>
>
> On Fri, 25 Mar 2016, Elliot S. MENKAH wrote:
>
> >
> > Hello Everyone,
> >
> > In reference to the papers Extracting convergent surface energies from
> slab calculations, 1996, and Surface e
> > nergies, work functions, and surface relaxations of low index metallic
> surfaces from first-principles, 2009,
> > I'm trying to compute surface energies with the Fiorentini-Methefessel
> technique.
> >
> > I'm extracting the bulk energy from a linear plot of total energy vrs N.
> >
> > I computed the total energies of nickel surface (100) with 12, 14, 16,
> > 18 and 20 atomic layers.
> >
> > I made a plot of total energies vrs N(Number of layers) and i got the
> > equation y = 0.24897 - 171.79x
> >
> > With the slope being -171.79, am I right to say the bulk energy is
> > -171.79Ry?
> >
> > Is this the right way of going about the Fiorentini-Methfessel technique?
> >
> > Can someone please point me in the right direction
> >
> > Thank you.
> >
> > Kind Regards,
> >
> > Elliot.
> >
> > --
> > Elliot Sarpong Menkah
> > Graduate Student - Computational Chemistry / Computational Material
> Science.
> > Theoretical and Computational Chemistry
> > Dept. of Chemistry
> > Kwame Nkrumah University of Science and Technology (KNUST),
> > Private Mail Bag,
> > Kumasi,
> > Ghana.
> > Mobile:+233-243-055-717,+233-202-929-058
> >
> >
> > Alt. Email: esmenkah at knust.edu.gh
> > elliotsmenkah at gmail.com
> > elliotsmenkah at hotmail.com
> >
> > webpage: http://chemistry.knust.edu.gh/MMC/group-members/ESMenkah
> >
> >
>
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>
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> End of Pw_forum Digest, Vol 104, Issue 24
> *****************************************
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>
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