[Pw_forum] Topic 8
Sunetra Das
sunetra.das.88 at gmail.com
Fri Feb 24 13:50:31 CET 2017
Thank you for your help, Mr. Jing Yang.
On 24 February 2017 at 16:30, <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
>
> 1. Re: Silicon 111 surface (Giovanni Cantele)
> 2. ESM Example (Al slab with bc2) and Otani/Sugino example
> (Louis Fry-Bouriaux)
> 3. Re: Symmetry recognition (Louis Fry-Bouriaux)
> 4. Re: Symmetry recognition (Paolo Giannozzi)
> 5. Re: Symmetry recognition (Louis Fry-Bouriaux)
> 6. Re: Symmetry recognition (Paolo Giannozzi)
> 7. (no subject) (Sunetra Das)
> 8. Charge is wrong error (Sunetra Das)
> 9. Re: Charge is wrong error (Jing Yang)
> 10. basis set module PROJWFC (alberto)
> 11. Re: About output of PDOS calculations of CeO2 (Giuseppe Mattioli)
> 12. Re: basis set module PROJWFC (Lorenzo Paulatto)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 23 Feb 2017 12:19:23 +0100
> From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> Subject: Re: [Pw_forum] Silicon 111 surface
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <46431764-885C-414F-8833-8087FE3E2308 at spin.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> this is the reply to the message you sent me, it is better for me to
> continue di discussion on PW_forum, being a way
> to share doubts, mistakes, problems with many other people that might help!
>
> You can build your Si(111) surface with any tool (by hand, using VNL, any
> other builder), but this tool will do just what
> you ask it to do, so before using the tool you ALWAYS need basic
> understanding. In this respect, I also suggest to look
> to the extensive documentation of Quantum-ESPRESSO and to the tutorials
> that are freely available in the web.
>
> Coming to your problem, Quantum-ESPRESSO, as you know, is based on plane
> waves, as such can only handle
> systems that are periodic in all three directions. If you need to simulate
> something that is periodic in only two, one or no
> direction in space (a surface, a 1D wire, a cluster/molecule/quantum dot
> respectively) you use the supercell approach.
>
> Let?s consider the case of a surface and let?s choose x and y as
> directions parallel to the surface, such that the z direction is orthogonal
> to it (you can make a different choice, of course).
>
> 1) In the x-y plane you have to identify the surface unit cell, spanned by
> two vectors a1 and a2 that describe the surface periodicity.
> Beware the choice of a1 and a2: they might be deduced from the bulk
> crystals or be more complicated if the surface
> is along special directions or if it undergoes some reconstruction.
>
> In the case of Si(111) you should first decide if you want to choose the
> minimal cell, or if you want to consider complex reconstruction
> (that is structures where one or more surface unit cells are gathered to
> build more complex structures) The minimal cell is obtained
> by considering the 111 plane of Si and trying to understand the
> periodicity vectors within that plane. The complex reconstruction are
> instead
> obtained once you know how many cells are gathered along the a1 and a2
> directions. For example, in the case of Si(111), whose structure
> had been long debated many years ago, it can undergo a 7x7 reconstruction
> (with a very large surface unit cell). You can find details wherever,
> for example this is one of the Google search results:
> http://nanowiz.tripod.com/sisteps/si111.htm <http://nanowiz.tripod.com/
> sisteps/si111.htm>
>
>
> 2) once the surface unit cell is identified, you must decide how many
> planes you want to consider in the direction (z-axis) orthogonal to the
> surface.
> In this case beware the fact that as you move in along z, you might meet
> one or more planes that are not equivalent to the 1st one. In other words,
> the second plane might not be obtained simply through a rigid shift along
> z of the 1st one, but there might be 2 or more planes before one equivalent
> to the first one is found
>
>
> 3) at this point you have the minimal number of atomic coordinates that,
> replicated along a1 and a2 reproduce a slab, that is, a Si(111) surface
> composed
> by a certain number of planes. How to choose a3 (this is one of the issues
> in your input file)? You measure the distance d along the z axis between
> the two furthermost planes
> AND and set the length of a3 to d+V, where V=vacuum space. The latter is
> needed because, in the supercell approach, you system is replicated
> also along a3, but you don?t want that periodic replicas interact with
> each other. The amount of V, let?s say 10 A (but a larger value might be
> needed), is chosen
> just to avoid interaction and convergence with respect to it must always
> be checked
>
>
> 4) because the z direction is not a true periodicity direction, if V is
> large enough you expect that the band dispersion is zero along the z
> direction, that is,
> you should obtain flat bands along that direction. As such, Brillouin zone
> sampling along that direction is useless, and the k-point grid you use for
> scf/relax
> calculations is in the form N x M x 1
>
>
> Whether you performs steps 1-4 by hand or using some tool such as VNL is
> up to you. I suggest to start with simple surfaces and simple crystals, to
> start with.
>
> Giovanni
>
> PS after writing this message, I have tried the Google search
> build surface supercell Quantum-ESPRESSO
> The 1st result is this link (I?m sure that many many others of interest
> for you show up!)
> http://www.democritos.it/events/pw-tutorial/lectures/pw-tutorial.pdf
> If I were you, I would start with the exercises described therein.
>
> > Actually sir I am trying to create a silicon 111 surface adsorbed by an
> Indium atom.To do this what should I be do first? The input file which I am
> using is create by the VNL GUI. Is there any other way to create a quantum
> espresso input file.
> > Thanx
> >
> >
> >> On 23 Feb 2017, at 10:18, Giovanni Cantele <
> giovanni.cantele at spin.cnr.it> wrote:
> >>
> >> 1) the atomic positions are likely wrong, I cannot understand what is
> the system you want to calculate. For example, the Si-In distance is 1.1 A,
> that looks
> >> very small. Try to look at your structure, opening the input file with
> XCrysDen. It is worth, before performing any further calculation, to check
> whether it is EXACTLY what you want.
> >>
> >>
> >> 2) in the case you would like to simulate the Si(111) SURFACE in the
> presence of In, your input does not correspond to a surface calculation.
> There is not vacuum space
> >> introduced between periodic replicas of the same slab, and there is
> k-point sampling in the direction orthogonal to the surface. If instead you
> are studying something like
> >> a Si heterostructure (e.g. a superlattice), please disregard this point
> >>
> >> 3) you are using ultra soft pseudo potential, the ecutwfc is likely too
> high (this however does not give convergence issues, but can make your
> calculation much slower
> >> than needed!). On the other hand, you are not setting the ecutrho
> variable, that by default is 4*ecutwfc. For ultrasoft pseudo potentials, as
> you might learn reading
> >> the relevant literature on the subject, a higher charge density cut-off
> is required, usually from 6 to 12 times ecutwfc
> >>
> >> 4) to improve convergence, increasing degauss might help, for systems
> very difficult to converge (but even in this case you should be aware of
> what degauss is and how to use it)
> >> and also decrease mixing_beta to 0.3, or 0.1 or maybe even less
> >>
> >>
> >> Giovanni
> >>
> >>
> >>
> >>> On 23 Feb 2017, at 06:59, Ubaid Mohd <onlymubaid at gmail.com <mailto:
> onlymubaid at gmail.com>> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I am trying to scf calculation of silicon(111)_Indium and the total
> force on the atom is not converging. Initially, the scf cycle itself was
> not converging.
> >>> What is wron with my input file.
> >>> Thanx,
> >>> Ubaid
> >>>
> >>>
> >>>
> >>>
> >>> Input File
> >>>
> >>>
> >>> &CONTROL
> >>> calculation='scf',
> >>> outdir='Pwscf',
> >>> prefix='Si_In',
> >>> pseudo_dir='.',
> >>> verbosity='low',
> >>> /
> >>>
> >>> &SYSTEM
> >>> ibrav=0,
> >>> celldm(1)=7.2565749368d0,
> >>> nat=7,
> >>> ntyp=2,
> >>> ecutwfc=90,
> >>> input_dft='PBE',
> >>> occupations='smearing',
> >>> smearing='mv',
> >>> degauss=0.005d0,
> >>> /
> >>>
> >>> &ELECTRONS
> >>> conv_thr=1d-06,
> >>> mixing_beta=0.7d0,
> >>> /
> >>>
> >>> ATOMIC_SPECIES
> >>> In 114.818000d0 In.pbe-d-rrkjus.UPF
> >>> Si 28.085500d0 Si.pbe-n-rrkjus_psl.0.1.UPF
> >>>
> >>> ATOMIC_POSITIONS {crystal}
> >>> Si 0.1708493746d0 0.3787081237d0 0.2302895286d0
> >>> Si 0.8375160412d0 0.7120414570d0 0.3136228619d0
> >>> Si 0.8375160412d0 0.7120414570d0 0.5636228619d0
> >>> Si 0.5041827079d0 1.0453747903d0 0.6469561953d0
> >>> Si 0.5041827079d0 1.0453747903d0 0.8969561953d0
> >>> Si 0.1708493746d0 0.3787081237d0 0.9802895286d0
> >>> In 0.2708493746d0 0.4787081237d0 0.3397104714d0
> >>>
> >>> K_POINTS {automatic}
> >>> 5 5 5 0 0 0
> >>>
> >>> CELL_PARAMETERS {alat}
> >>> 1.000000000000d0 0.000000000000d0 0.000000000000d0
> >>> -0.500000000000d0 0.866025403784d0 0.000000000000d0
> >>> 0.000000000000d0 0.000000000000d0 2.449489742783d0
> >>>
> >>>
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at pwscf.org <mailto: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 <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
> >> 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: Thu, 23 Feb 2017 12:42:04 +0000
> From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> Subject: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino
> example
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID:
> <DB5PR0301MB1942FC78116BD10A9A9B72C49E530 at DB5PR0301MB1942.
> eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi there,
>
>
> I am trying to understand the ESM example with bc2 (metal-slab-metal)
> distributed with QE 6.0 which consists of an Al(001) slab between two
> electrodes, and at the same time I am trying to replicate the results of
> Otani and Sugino in their paper (Phys. Rev. B, 73, 115407, 2006) which
> consists of an Al/Si(111)/Al slab between two screening boundaries.
>
>
> I have a few questions:
>
>
> ** 1. ** In the QE example the following cell params and atomic positions
> are specified:
>
>
> CELL_PARAMETERS bohr
> 10.82227686 0.00000000 0.00000000
> 0.00000000 10.82227686 0.00000000
> 0.00000000 0.00000000 22.67672253
> ATOMIC_POSITIONS bohr
> Al 0.00000000 0.00000000 0.00000000
> Al 5.41113843 0.00000000 0.00000000
> Al 0.00000000 5.41113843 0.00000000
> Al 5.41113843 5.41113843 0.00000000
>
>
> My understanding is that the cell will repeat without overlapping atoms
> along X and Y. What I'm not clear on is why the 3rd lattice vector is so
> large?
>
>
> The parameter 'esm_w' defaults to zero and is not specified in the
> example, so does this large value mean that there is a region of vacuum? Or
> does it just repeat the atoms such that in the Z-direction there are 5 Al
> layers? I'm guessing that this 3rd cell parameter Z-value corresponds to
> L_z, which in the paper corresponds to z_0?
>
>
> ** 2. ** I have reproduced the 'surface unit cell' from Otani/Sugino's
> paper using VESTA.
>
>
> My concern here is with the correct repetition of atoms in X and Y, and
> what exactly happens with the Z direction. I realize I must first rotate
> the unit cell such that the repeated Al atoms lie perpendicular to the Z
> Cartesian axis which I have not done yet.
>
>
> I have tested the repetition of this cell within VESTA along vectors
> perpendicular to the Al plane. So my most important question is: if the
> height of the cell along Z is ~14.4281 Angstrom (measured from Al center
> plane), then the third 'CELL_PARAMETERS' entry (after rotation) should be
> this value exactly + the 'decay length' of the wavefunction in Z? Then the
> parameter 'esm_w' is used to set z_1 from the paper I suppose?
>
>
> I will generate an xyz file of the surface cell, but if I repeat by 3.816
> A along a surface lattice vector, it is a matter of just deleting the
> entries that cause an overlap of the atoms I suppose?
>
>
> Thank you for your time and sorry for the very long email,
>
> Kindest regards,
>
> Louis
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 23 Feb 2017 19:02:05 +0000
> From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> Subject: Re: [Pw_forum] Symmetry recognition
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <DB5PR0301MB1942D7D22B680834994E9D779E530 at DB5PR0301MB1942.
> eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Pascal,
>
>
> When I first started using QE 6.0 not long ago I had trouble using
> crystal_sg, I suppose you have the Wyckoff positions of your atoms. What I
> did was use the VESTA program which allows you to input Wyckoff positions
> and it will correctly generate the cell as long as other options are
> correct. I then exported to an xyz file and converted the coordinates in
> angstroms to internal crystal coordinates ('crystal' option) using:
>
> https://en.wikipedia.org/wiki/Fractional_coordinates
>
> Fractional coordinates - Wikipedia<https://en.
> wikipedia.org/wiki/Fractional_coordinates>
> en.wikipedia.org
> In crystallography, a fractional coordinate system is a coordinate system
> in which the edges of the unit cell are used as the basic vectors to
> describe the positions ...
>
>
> Which worked perfectly for me. This is easily done with a Python script or
> something similar!
>
>
> Kindest regards,
>
> Louis
>
> ________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
> of Pascal Boulet <pascal.boulet at univ-amu.fr>
> Sent: 23 February 2017 07:56:16
> To: PWSCF Forum
> Subject: [Pw_forum] Symmetry recognition
>
> Dear all,
>
> I am running a structural optimization with QE 6.0. The structure is
> orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not
> converge so I have to restart it. But as I restart it, the number of
> symmetry is now 4, there is a descent of symmetry. I shall say that I use
> the space_group option with COORDINATES crystal_sg. But the problem remains
> if I put all the coordinates (unsurprisingly).
>
> Is there a reason for this, and can I avoid this?
>
> Thank you
> Best regards
> Pascal
>
> -
> Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE
> Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie Niemen
> - 13013 Marseille
> T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire<
> http://amu.fr/pages_web_BOULET_PASCAL/annuaire> - Email :
> pascal.boulet at univ-amu.fr<mailto:pascal.boulet at univ-amu.fr>
>
>
>
>
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> ------------------------------
>
> Message: 4
> Date: Thu, 23 Feb 2017 21:04:21 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Symmetry recognition
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCtz160Sd8rySjBC67s2SHhTOcmNViZ3=RJLjzL8-z6LTQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Thu, Feb 23, 2017 at 8:02 PM, Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> wrote:
>
> When I first started using QE 6.0 not long ago I had trouble using
> > crystal_sg
> >
>
> Why?
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> ------------------------------
>
> Message: 5
> Date: Thu, 23 Feb 2017 20:12:52 +0000
> From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> Subject: Re: [Pw_forum] Symmetry recognition
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <DB5PR0301MB19424D8B5FDB86E577B109189E530 at DB5PR0301MB1942.
> eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hey Paolo,
>
>
> I gave up as it wouldn't parse the input I provided, it was definitely
> my fault, so I gave up and used the method I described which worked fine. I
> didn't mean to imply there was a problem with the software, sorry about
> that.
>
>
> Louis
>
> ________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
> of Paolo Giannozzi <p.giannozzi at gmail.com>
> Sent: 23 February 2017 20:04:21
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Symmetry recognition
>
> On Thu, Feb 23, 2017 at 8:02 PM, Louis Fry-Bouriaux <ellf at leeds.ac.uk
> <mailto:ellf at leeds.ac.uk>> wrote:
>
> When I first started using QE 6.0 not long ago I had trouble using
> crystal_sg
>
> Why?
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> ------------------------------
>
> Message: 6
> Date: Thu, 23 Feb 2017 21:45:36 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Symmetry recognition
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCtiYOpZxFHY0H+-xFJb2c=a+5dM15xO0C_LB4LRH4+uqw at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Of course there is a reason, but not necessarily a good one. If you
> are "restarting from an incomplete calculation", I guess that the code
> overwrites the input coordinates with the current ones. The symmetry
> should be the same, but sometimes numerical noise breaks the symmetry.
> It is impossible to say more without an example.
>
> Paolo
>
> On Thu, Feb 23, 2017 at 8:56 AM, Pascal Boulet
> <pascal.boulet at univ-amu.fr> wrote:
> > Dear all,
> >
> > I am running a structural optimization with QE 6.0. The structure is
> > orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not
> > converge so I have to restart it. But as I restart it, the number of
> > symmetry is now 4, there is a descent of symmetry. I shall say that I use
> > the space_group option with COORDINATES crystal_sg. But the problem
> remains
> > if I put all the coordinates (unsurprisingly).
> >
> > Is there a reason for this, and can I avoid this?
> >
> > Thank you
> > Best regards
> > Pascal
> >
> > -
> > Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE
> > Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie
> Niemen -
> > 13013 Marseille
> > T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
> > Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire -
> Email :
> > pascal.boulet at univ-amu.fr
> >
> >
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 24 Feb 2017 11:32:45 +0530
> From: Sunetra Das <sunetra.das.88 at gmail.com>
> Subject: [Pw_forum] (no subject)
> To: pw_forum at pwscf.org
> Message-ID:
> <CAPLukqnb5yf+k8-EmkMwitWeiGZcx_PrasB1MRigfGyRwBe9Sg at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello everybody
> I am getting wrong charge error as given below, in my output file:
>
>
>
>
>
>
>
>
>
> * WARNING: integrated charge= 6.02151254, expected=
> 6.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> Error in routine electrons (1): charge is
> wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> stopping ...*
>
> I have checked the FAQ section of QE website where the solution is given as
> to use a gaussian smearing. I am using a gaussian smearing for my metallic
> system, still the error.
>
> I am copying my input file contents below:
>
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> * &CONTROL calculation = 'vc-relax' ,
> restart_mode = 'from_scratch' , outdir = './tmp'
> , pseudo_dir = '/home/sunetra/Desktop/In_qe/'
> , prefix = 'In_vc-relax' , lkpoint_dir
> = .true. , verbosity = 'high' ,
> tstress = .true. , tprnfor = .true. ,
> forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10
> , / &SYSTEM ibrav = 0, nat =
> 2, ntyp = 1, ecutwfc = 30
> , nbnd = 10, occupations =
> 'smearing' , degauss = 0.06 ,
> smearing = 'gaussian' , input_dft = 'PBE'
> , / &ELECTRONS electron_maxstep = 3000,
> scf_must_converge = .true. , conv_thr = 1D-10
> , mixing_beta = 0.7 , mixing_mode = 'plain'
> , mixing_ndim = 8 , diagonalization = 'cg'
> , diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS
> Angstrom 4.953665310 0.000000000 0.000000000 2.476832660
> 4.290000000 0.000000000 0.000000000 0.000000000 20.000000000
> ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom
> In 2.476832660 1.430000000 0.000000000 In
> 4.953665310 2.860000000 0.000000000 K_POINTS automatic 31 31 1
> 0 0 0 *
> Kindly guide me in this matter. Thank you.
> Regards,
> Sunetra Das
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> ------------------------------
>
> Message: 8
> Date: Fri, 24 Feb 2017 11:41:07 +0530
> From: Sunetra Das <sunetra.das.88 at gmail.com>
> Subject: [Pw_forum] Charge is wrong error
> To: pw_forum at pwscf.org
> Message-ID:
> <CAPLukqm1kSk-VFg7eMjJGPmHVeZfUwK=0qZW+
> nRxuVF5SC+4YA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello everybody
> I am getting wrong charge error as given below, in my output file:
>
>
>
>
>
>
>
>
>
> * WARNING: integrated charge= 6.02151254, expected=
> 6.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> Error in routine electrons (1): charge is
> wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> stopping ...*
>
> I have checked the FAQ section of QE website where the solution is given as
> to use a gaussian smearing. I am using a gaussian smearing for my metallic
> system, still the error.
> I am using QE version 5.0.3. Also the error occurs after several
> iterations.
> I am copying my input file contents below:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> * &CONTROL calculation = 'vc-relax' ,
> restart_mode = 'from_scratch' , outdir = './tmp'
> , pseudo_dir = '/home/sunetra/Desktop/In_qe/'
> , prefix = 'In_vc-relax' , lkpoint_dir
> = .true. , verbosity = 'high' ,
> tstress = .true. , tprnfor = .true. ,
> forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10
> , / &SYSTEM ibrav = 0, nat =
> 2, ntyp = 1, ecutwfc = 30
> , nbnd = 10, occupations =
> 'smearing' , degauss = 0.06 ,
> smearing = 'gaussian' , input_dft = 'PBE'
> , / &ELECTRONS electron_maxstep = 3000,
> scf_must_converge = .true. , conv_thr = 1D-10
> , mixing_beta = 0.7 , mixing_mode = 'plain'
> , mixing_ndim = 8 , diagonalization = 'cg'
> , diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS
> Angstrom 4.953665310 0.000000000 0.000000000 2.476832660
> 4.290000000 0.000000000 0.000000000 0.000000000 20.000000000
> ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom
> In 2.476832660 1.430000000 0.000000000 In
> 4.953665310 2.860000000 0.000000000 K_POINTS automatic 31 31 1
> 0 0 0 *
> Kindly can anyone please guide me in this matter? Thank you.
> Regards,
> Sunetra Das
> -------------- next part --------------
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> ------------------------------
>
> Message: 9
> Date: Fri, 24 Feb 2017 01:54:43 -0500
> From: Jing Yang <yang15 at sas.upenn.edu>
> Subject: Re: [Pw_forum] Charge is wrong error
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <137AC56B-A1F5-4A32-88DE-44090A4A5D72 at sas.upenn.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> In some cases, this indicates your pseudopotential is not good or initial
> configuration is wrong ... Try use a different pseudopotential then.
>
> Thanks,
> Jing Yang
>
> > On Feb 24, 2017, at 1:11 AM, Sunetra Das <sunetra.das.88 at gmail.com>
> wrote:
> >
> > Hello everybody
> > I am getting wrong charge error as given below, in my output file:
> >
> > WARNING: integrated charge= 6.02151254, expected= 6.00000000
> >
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> > Error in routine electrons (1):
> > charge is wrong
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> >
> > stopping ...
> >
> > I have checked the FAQ section of QE website where the solution is given
> as to use a gaussian smearing. I am using a gaussian smearing for my
> metallic system, still the error.
> > I am using QE version 5.0.3. Also the error occurs after several
> iterations.
> > I am copying my input file contents below:
> >
> > &CONTROL
> > calculation = 'vc-relax' ,
> > restart_mode = 'from_scratch' ,
> > outdir = './tmp' ,
> > pseudo_dir = '/home/sunetra/Desktop/In_qe/' ,
> > prefix = 'In_vc-relax' ,
> > lkpoint_dir = .true. ,
> > verbosity = 'high' ,
> > tstress = .true. ,
> > tprnfor = .true. ,
> > forc_conv_thr = 1.0D-2 ,
> > etot_conv_thr = 10.0D-10 ,
> >
> > /
> > &SYSTEM
> > ibrav = 0,
> > nat = 2,
> > ntyp = 1,
> > ecutwfc = 30 ,
> > nbnd = 10,
> > occupations = 'smearing' ,
> > degauss = 0.06 ,
> > smearing = 'gaussian' ,
> > input_dft = 'PBE' ,
> > /
> > &ELECTRONS
> > electron_maxstep = 3000,
> > scf_must_converge = .true. ,
> > conv_thr = 1D-10 ,
> > mixing_beta = 0.7 ,
> > mixing_mode = 'plain' ,
> > mixing_ndim = 8 ,
> > diagonalization = 'cg' ,
> > diago_cg_maxiter = 3000 ,
> > /
> > &ions
> > /
> > &cell
> > /
> > CELL_PARAMETERS Angstrom
> > 4.953665310 0.000000000 0.000000000
> > 2.476832660 4.290000000 0.000000000
> > 0.000000000 0.000000000 20.000000000
> > ATOMIC_SPECIES
> > In 114.81800 In.pbe-hgh.UPF
> > ATOMIC_POSITIONS Angstrom
> > In 2.476832660 1.430000000 0.000000000
> > In 4.953665310 2.860000000 0.000000000
> > K_POINTS automatic
> > 31 31 1 0 0 0
> >
> > Kindly can anyone please guide me in this matter? Thank you.
> > Regards,
> > Sunetra Das
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 10
> Date: Fri, 24 Feb 2017 10:09:00 +0100
> From: alberto <voodoo.bender at gmail.com>
> Subject: [Pw_forum] basis set module PROJWFC
> To: pw_forum at pwscf.org
> Message-ID:
> <CAJKZiECH-kcJkiyC_TNxKUTsdLknfKHCgS2P9Zssy+
> 7GoD7WOA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I have a question about the projections of band structure with *PROJWFC.
> *what
> basis set is used for the creation of the projections of the bands (e.g.,
> double zeta, triple zeta, etc.)? In particular my model have got Sn and I.
>
> Al
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>
> ------------------------------
>
> Message: 11
> Date: Fri, 24 Feb 2017 10:36:03 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Subject: Re: [Pw_forum] About output of PDOS calculations of CeO2
> To: pw_forum at pwscf.org
> Message-ID: <36291620.ELma9kdhud at amore2>
> Content-Type: text/plain; charset="ISO-8859-1"
>
>
> Dear Phanikumar
>
> PDOS is not affected by orbital occupation. Occupied orbitals in your plot
> are those below the Fermi level of your system, which is printed in the pw.x
> output.
> HTH
> Giuseppe
>
> On Thursday, February 23, 2017 11:52:01 AM Phanikumar Pentyala wrote:
> > Thank you Giuseppe Mattioli and Paolo Giannozzi
> >
> > The order of orbitals it calculates energy values already discussed by
> > Paolo Giannozzi. But, in my system it contains *4f* have 7 orbitals in
> it.
> > but all will not fill during electron localizations (only first two
> > orbitals). so my doubt was what is the use of remaining line of values in
> > above attached document and which orbital values I have to choose in my
> > graph?
> >
> > Please bare with my technical knowledge because I am not a background
> from
> > science
> >
> > Thank you once again
> >
> >
> > Regards
> > Phanikumar
> >
> >
> > On Wed, Feb 22, 2017 at 7:14 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
> >
> > wrote:
> > > The order of Y_{lm}(\theta,\phi) is described here:
> > > http://www.quantum-espresso.org/wp-content/uploads/Doc/pp_
> > > user_guide/node8.html
> > > For l=3 the sequence continues with: P_{3,0}, P_{3,1}cos(\phi),
> > > P_{3,1}sin(\phi), P_{3,2}cos(2\phi), P_{3,2}sin(2\phi),
> > > P_{3,3}cos(3\phi), P_{3,3}sin(3\phi)
> > >
> > > Paolo
> > >
> > > On Wed, Feb 22, 2017 at 2:16 PM, Giuseppe Mattioli
> > >
> > > <giuseppe.mattioli at ism.cnr.it> wrote:
> > > > Dear Phanikumar
> > > > If I understand well your question, the pdos file attached to your
> > >
> > > previous message should contain 9 columns: the energy scale of PDOS,
> the
> > > total 4f
> > >
> > > > PDOS and the PDOS of the seven 4f orbitals (if you sum column 3-9 you
> > >
> > > obtain column 2). As opposed to the l=1 and l=2 cases, the symmetry
> order of
> > >
> > > > orbitals in the l=3 case is not reported in the projwfc manual, but
> > >
> > > maybe there is someone more skilled than me that know the right
> order...
> > >
> > > > HTH
> > > > Giuseppe
> > > >
> > > > On Wednesday, February 22, 2017 05:18:40 PM Phanikumar Pentyala
> wrote:
> > > >> Thnk you Lorenzo Paulatto for quick reply
> > > >>
> > > >> Yes I am doing DFT+U calculations. 4f will be in the valance bands
> of Ce
> > > >> atom. Because of redox property of *Ce*, electron localization take
> > >
> > > place.
> > >
> > > >> Here I am attaching my out put file of PDOS. Also I am using GGA
> (PBE)
> > > >> functional, NORM-CONSERVING potentials for my calculation.
> > > >>
> > > >>
> > > >> On Wed, Feb 22, 2017 at 5:02 PM, Lorenzo Paulatto <
> > > >>
> > > >> lorenzo.paulatto at impmc.upmc.fr> wrote:
> > > >> > On Wednesday, February 22, 2017 12:18:31 PM CET Phanikumar
> Pentyala
> > >
> > > wrote:
> > > >> > > My doubt was, cerium electronic structure have only single or
> double
> > > >> > > electron in *f* shell, so can I choose third or fourth line of
> PDOS
> > > >> >
> > > >> > output
> > > >> >
> > > >> > > file or last line (first line belongs to LDOS)?
> > > >> >
> > > >> > Dear Phanikumar,
> > > >> > the pseudopotential you are using for Cerium may or may not have
> the f
> > > >> > electron in valence.
> > > >> >
> > > >> > If the electron is in valence you will have a corresponding file
> > >
> > > after the
> > >
> > > >> > projwfc calculation. But your system will probably be metallica
> and
> > >
> > > have
> > >
> > > >> > all
> > > >> > sort of problems, unless you use DFT+U and know what you are
> doing.
> > > >> >
> > > >> > If it is in the core, you won't be able to compute its pdos (which
> > >
> > > anyway,
> > >
> > > >> > is
> > > >> > a delta function at the atomic state energy). Also your valence
> bands
> > >
> > > will
> > >
> > > >> > miss some feature and probably be not completely correct.
> > > >> > On the other hand, you will be able to get the calculation working
> > >
> > > without
> > >
> > > >> > too
> > > >> > much fiddling.
> > > >> >
> > > >> >
> > > >> > hth
> > > >> >
> > > >> > --
> > > >> > Dr. Lorenzo Paulatto
> > > >> > IdR @ IMPMC -- CNRS & Universit? Paris 6
> > > >> > phone: +33 (0)1 442 79822 / skype: paulatz
> > > >> > www: http://www-int.impmc.upmc.fr/~paulatto/
> > > >> > mail: 23-24/423 Bo?te courrier 115, 4 place Jussieu 75252 Paris
> > >
> > > C?dex 05
> > >
> > > >> > _______________________________________________
> > > >> > Pw_forum mailing list
> > > >> > Pw_forum at pwscf.org
> > > >> > http://pwscf.org/mailman/listinfo/pw_forum
> > > >
> > > > ********************************************************
> > > > - 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 90672342 - Fax +39 06 90672316
> > > > E-mail: <giuseppe.mattioli at ism.cnr.it>
> > > > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
> > > > ResearcherID: F-6308-2012
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://pwscf.org/mailman/listinfo/pw_forum
> > >
> > > --
> > > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> > > Univ. 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
> > > http://pwscf.org/mailman/listinfo/pw_forum
>
> ********************************************************
> - 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 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
> ResearcherID: F-6308-2012
>
>
>
> ------------------------------
>
> Message: 12
> Date: Fri, 24 Feb 2017 10:50:41 +0100
> From: Lorenzo Paulatto <lorenzo.paulatto at impmc.upmc.fr>
> Subject: Re: [Pw_forum] basis set module PROJWFC
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1966835.skiQF9jZZP at naquite>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Friday, February 24, 2017 10:09:00 AM CET alberto wrote:
> > I have a question about the projections of band structure with *PROJWFC.
> > *what basis set is used for the creation of the projections of the bands
> > (e.g., double zeta, triple zeta, etc.)? In particular my model have got
> Sn
> > and I.
>
> Dear Alberto,
> projwfc.x projects on the atomic wavefunctions that are included in the
> pesudopotential file. Check the header of the file to have more details.
>
> kind regards
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Universit? Paris 6
> phone: +33 (0)1 442 79822 / skype: paulatz
> www: http://www-int.impmc.upmc.fr/~paulatto/
> mail: 23-24/423 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
> End of Pw_forum Digest, Vol 115, Issue 24
> *****************************************
>
>
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