[Pw_forum] Pw_forum Digest, Vol 115, Issue 25
hamid elbushra
hamidelbushra80 at gmail.com
Sat Feb 25 14:14:57 CET 2017
Hello for all
so l need the in put of TiO2 ( bluk)
Thanks
بتاريخ ٢٥/٠٢/٢٠١٧ ٢:٠٠ م، جاء من <pw_forum-request at pwscf.org>:
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> Today's Topics:
>
> 1. Re: Topic 8 (Sunetra Das)
> 2. Re: ESM Example (Al slab with bc2) and Otani/Sugino example
> (Minoru Otani)
> 3. Re: Symmetry recognition (Pascal Boulet)
> 4. Re: ESM Example (Al slab with bc2) and Otani/Sugino example
> (Louis Fry-Bouriaux)
> 5. All Lowdin charges are zero (Semen Yesylevskyy)
> 6. Re: All Lowdin charges are zero (Giuseppe Mattioli)
> 7. Re: All Lowdin charges are zero (Semen Yesylevskyy)
> 8. Re: All Lowdin charges are zero (Giuseppe Mattioli)
> 9. Error in routine phq_readin (5010) (Sunetra Das)
> 10. Re: All Lowdin charges are zero (Semen Yesylevskyy)
> 11. Re: Error in routine phq_readin (5010) (Louis Fry-Bouriaux)
> 12. MaX user portal and newsletter (Andrea Ferretti)
> 13. Re: Error in routine phq_readin (5010) (Paolo Giannozzi)
> 14. Re: Error in routine phq_readin (5010) (dario rocca)
> 15. Re: Error in routine phq_readin (5010) (Louis Fry-Bouriaux)
> 16. Re: Error in routine phq_readin (5010) (Lorenzo Paulatto)
> 17. MaX user portal and newsletter (fwd) (Andrea Ferretti)
> 18. The unit of potential (??)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 24 Feb 2017 18:20:31 +0530
> From: Sunetra Das <sunetra.das.88 at gmail.com>
> Subject: Re: [Pw_forum] Topic 8
> To: pw_forum at pwscf.org
> Message-ID:
> <CAPLukqmjD6jr4U4ZOZ6Q_RBvpVMcAvuf1GzY4NR6DgnkqvA_RQ@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Thank you for your help, Mr. Jing Yang.
>
> On 24 February 2017 at 16:30, <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
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > 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
> >
> > -------------- next part --------------
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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
> >
> > -------------- next part --------------
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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>
> >
> >
> >
> >
> > -------------- next part --------------
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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?
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170223/
> > e61d2cfd/attachment-0001.html
> >
> > ------------------------------
> >
> > 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:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * &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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
> > d49cd209/attachment-0001.html
> >
> > ------------------------------
> >
> > 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 --------------
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
> > db4ef4fd/attachment-0001.html
> >
> > ------------------------------
> >
> > 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 --------------
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
> > 6d059f17/attachment-0001.html
> >
> > ------------------------------
> >
> > 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
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
> > 330bddc5/attachment-0001.html
> >
> > ------------------------------
> >
> > 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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> ------------------------------
>
> Message: 2
> Date: Fri, 24 Feb 2017 23:24:31 +0900
> From: Minoru Otani <minoru.otani at aist.go.jp>
> Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and
> Otani/Sugino example
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <138FACE9-ECDC-4FD8-B88A-1869212621C1 at aist.go.jp>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Louis,
>
> Thank you for using the ESM. The figure 1 in the paper shows how does the
> unit cell place in the z-direction. As you see, we need to put enough
> vacuum region on both sides of a slab. Accordingly, the 3rd cell parameter
> (Lz) becomes large. The z0 is not equal to Lz but equal to Lz/2.
>
> There are some example calculations in ESM_examle directory. I recommend
> you to have a look at the Aluminum (001) slab calculations with various
> boundary conditions.
>
> Best regards,
> Minoru
>
> ------------------------------------------------------------
> --------------------------------------------
> Minoru Otani
> National Institute of Advanced Industrial Science and Technology
> Research Centre for Computational Design of Advanced Functional Materials
> email : minoru.otani at aist.go.jp <mailto:minoru.otani at aist.go.jp>
> ------------------------------------------------------------
> ---------------------------------------------
>
> > On Feb 23, 2017, at 21:42, Louis Fry-Bouriaux <ellf at leeds.ac.uk> wrote:
> >
> > 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
> >
> > _______________________________________________
> > 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>
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 24 Feb 2017 15:44:25 +0100
> From: Pascal Boulet <pascal.boulet at univ-amu.fr>
> Subject: Re: [Pw_forum] Symmetry recognition
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <89481035-37BD-45FD-9665-1F4E49FBDD9F at univ-amu.fr>
> Content-Type: text/plain; charset=windows-1252
>
> Dear all,
>
> Thank you for your answers. I am trying to reproduce it with a smaller
> system? I indeed restart from an incomplete calculation.
>
> Pascal
>
>
>
> Le 23 f?vr. 2017 ? 21:45, Paolo Giannozzi <p.giannozzi at gmail.com> a ?crit
> :
>
> > 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
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 24 Feb 2017 15:14:30 +0000
> From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and
> Otani/Sugino example
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <DB5PR0301MB194286ED6BC8DB80EFB586B19E520 at DB5PR0301MB1942.
> eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Minoru,
>
>
> Thank you for clarifying! I will proceed to calculate, is it worth
> making a QE example for this? It would be quite nice to have your result in
> there!
>
>
> Kindest regards,
>
> Louis
>
> ________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
> of Minoru Otani <minoru.otani at aist.go.jp>
> Sent: 24 February 2017 14:24:31
> To: PWSCF Forum
> Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino
> example
>
> Dear Louis,
>
> Thank you for using the ESM. The figure 1 in the paper shows how does the
> unit cell place in the z-direction. As you see, we need to put enough
> vacuum region on both sides of a slab. Accordingly, the 3rd cell parameter
> (Lz) becomes large. The z0 is not equal to Lz but equal to Lz/2.
>
> There are some example calculations in ESM_examle directory. I recommend
> you to have a look at the Aluminum (001) slab calculations with various
> boundary conditions.
>
> Best regards,
> Minoru
>
> ------------------------------------------------------------
> --------------------------------------------
> Minoru Otani
> National Institute of Advanced Industrial Science and Technology
> Research Centre for Computational Design of Advanced Functional Materials
> email : minoru.otani at aist.go.jp<mailto:minoru.otani at aist.go.jp>
> ------------------------------------------------------------
> ---------------------------------------------
>
> On Feb 23, 2017, at 21:42, Louis Fry-Bouriaux <ellf at leeds.ac.uk<mailto:
> ellf at leeds.ac.uk>> wrote:
>
>
> 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
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
> http://pwscf.org/mailman/listinfo/pw_forum
>
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> URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
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>
> ------------------------------
>
> Message: 5
> Date: Fri, 24 Feb 2017 18:30:47 +0300
> From: Semen Yesylevskyy <yesint at mail.ru>
> Subject: [Pw_forum] All Lowdin charges are zero
> To: pw_forum at pwscf.org
> Message-ID: <1487950247.124921620 at f401.i.mail.ru>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
> I'm new to QE so please forgive if I'm missing something very obvious. I'm
> trying to study the charge transfer between organic molecules and MoS2
> monolayer. I optimized the system, did an scf and then tried to get Lowdin
> charges with projwcf. However, all charges are almost zero which is not
> what I can expect:
>
> Lowdin Charges:
> ??? ?
> ???? Atom #?? 1: total charge =?? 0.0000, s =? 0.0000,
> ???? Atom #?? 1: total charge =?? 0.0000, p =? 0.0000, pz=? 0.0000, px=?
> 0.0000, py=? 0.0000,
> ???? Atom #?? 2: total charge =?? 0.0001, s =? 0.0000,
> ???? Atom #?? 2: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=?
> 0.0000, py=? 0.0000,
> ???? Atom #?? 3: total charge =?? 0.0001, s =? 0.0000,
> ???? Atom #?? 3: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=?
> 0.0000, py=? 0.0000,
> ???? Atom #?? 4: total charge =?? 0.0000, s =? 0.0000,
> ???? Atom #?? 4: total charge =?? 0.0000, p =? 0.0000, pz=? 0.0000, px=?
> 0.0000, py=? 0.0000,
> ???? Atom #?? 5: total charge =?? 0.0001, s =? 0.0000,
> ???? Atom #?? 5: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=?
> 0.0000, py=? 0.0000,
> ???? Atom #?? 6: total charge =?? 0.0001, s =? 0.0000,
> ....
>
> Could you please give me some advice of what I'm doing wrong?
>
> --------------------------------
> The projwcf input:
>
> ?&PROJWFC
> ????????????????????? prefix = './3cell-cb_scf' ,
> ????????????????????? outdir = '.' ,
> ????????????????????? ngauss = 0.1 ,
> ????????????????????? DeltaE = 0.01 ,
> ?/
>
> --------------------------------
> The scf input:
>
> ?&CONTROL
> ???????????????? calculation = 'scf' ,
> ??????????????? restart_mode = 'from_scratch' ,
> ????????????????????? outdir = '.' ,
> ????????????????????? wfcdir = './tmp' ,
> ????????????????? pseudo_dir = '.' ,
> ????????????????????? prefix = '3cell-cb_scf' ,
> ?????????????????????? nstep = 1000 ,
> ???????????????????? tstress = .false. ,
> ?/
> ?&SYSTEM
> ?????????????????????? ibrav = 4 ,
> ?????????????????????????? A = 9.495 ,
> ?????????????????????????? B = 9.495 ,
> ?????????????????????????? C = 100.0 ,
> ?????????????????????? cosAB = 0.5 ,
> ?????????????????????? cosAC = 0 ,
> ?????????????????????? cosBC = 0 ,
> ???????????????????????? nat = 39,
> ??????????????????????? ntyp = 5,
> ???????????????????? ecutwfc = 35 ,
> ???????????????????? ecutrho = 140 ,
> ?????????????????????? nosym = .true. ,
> ????????????????? tot_charge = 0.000000 ,
> ?/
> ?&ELECTRONS
> ??????????? electron_maxstep = 200 ,
> ??????????? scf_must_converge = .false. ,
> ??????????? diagonalization='cg' ,
> ?/
> ?&IONS
> ??????????????? ion_dynamics = 'bfgs' ,
> ?/
> ATOMIC_SPECIES
> ?? Mo?? 95.96?? Mo_ONCV_PBE-1.0.upf
> ??? S?? 32.06?? S_pbe_v1.2.uspp.F.UPF
> ??? C?? 12.011? C_pbe_v1.2.uspp.F.UPF
> ??? H?? 1.008?? H.pbe-rrkjus_psl.0.1.UPF
> ?? Cl?? 35.45?? cl_pbe_v1.4.uspp.F.UPF
> ATOMIC_POSITIONS angstrom
> Mo?????? 1.392123361?? 1.675146760?? 5.927158394
> S??????? 1.409356288?? 3.492127081?? 4.353797199
> S??????? 1.409009361?? 3.492914431?? 7.500696022
> Mo?????? 2.974783806?? 4.416004278?? 5.927352435
> S??????? 2.991861295?? 6.232688291?? 4.353114990
> S??????? 2.991733615?? 6.233889787?? 7.500216780
> Mo?????? 4.557309411?? 7.156655993?? 5.926482117
> S??????? 4.574550104?? 8.974187415?? 4.353268832
> S??????? 4.573865790?? 8.974308816?? 7.499997172
> Mo?????? 4.556900653?? 1.675497042?? 5.926861427
> S??????? 4.573955171?? 3.492114510?? 4.352949498
> S??????? 4.574377417?? 3.492858021?? 7.500504130
> Mo?????? 6.139333906?? 4.416035304?? 5.926363713
> S??????? 6.156932316?? 6.232998289?? 4.352535948
> S??????? 6.156651090?? 6.233324282?? 7.500124138
> Mo?????? 7.721896396?? 7.156797182?? 5.926687354
> S??????? 7.739160210?? 8.974228888?? 4.353457824
> S??????? 7.739048493?? 8.974459743?? 7.500654977
> Mo?????? 7.722031044?? 1.675217921?? 5.926454615
> S??????? 7.739331052?? 3.492171149?? 4.352920557
> S??????? 7.738377057?? 3.492639347?? 7.499947690
> Mo?????? 9.304280720?? 4.416123626?? 5.927097215
> S??????? 9.321652087?? 6.232837357?? 4.353059451
> S??????? 9.321594176?? 6.234116854?? 7.500174405
> Mo????? 10.887047440?? 7.156845127?? 5.926347019
> S?????? 10.903965611?? 8.974283787?? 4.353226240
> S?????? 10.903829602?? 8.974680010?? 7.500128022
> C??????? 5.700416780?? 4.960942076? 11.705590151
> C??????? 5.786661978?? 6.354516349? 11.705273773
> C??????? 7.046391983?? 6.956535202? 11.705217371
> C??????? 8.203237318?? 6.173116561? 11.705190411
> C??????? 8.099168585?? 4.780492709? 11.705023203
> C??????? 6.846678887?? 4.164104064? 11.704869934
> Cl?????? 4.129012811?? 4.204270654? 11.705957792
> H??????? 4.877613854?? 6.955359406? 11.704377918
> H??????? 7.118320846?? 8.046628444? 11.704165169
> H??????? 9.184749419?? 6.647034640? 11.704328004
> H??????? 8.998646725?? 4.161998637? 11.704137157
> H??????? 6.757143341?? 3.077849963? 11.704290956
> K_POINTS automatic
> ? 1 1 1?? 1 1 1
>
>
>
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>
> ------------------------------
>
> Message: 6
> Date: Fri, 24 Feb 2017 16:44:35 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Subject: Re: [Pw_forum] All Lowdin charges are zero
> To: pw_forum at pwscf.org
> Message-ID: <8934804.clCi8xVGCZ at amore2>
> Content-Type: text/plain; charset="ISO-8859-1"
>
>
>
> Dear Colleague (please sign always the posts with name and affiliation)
>
> ONCV PPs do not contain pseudowavefunctions, if you do not say to the
> Hamann's code to include them.
> Look for this old thread in the QE forum
>
> [Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc
>
> That should contain all you need to rebuild a PP with wfcs and to obtain
> Lowdin charges with projwfc.x
>
> HTH
> Giuseppe
>
>
> On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:
> > Dear All,
> > I'm new to QE so please forgive if I'm missing something very obvious.
> I'm trying to study the charge transfer between organic molecules and MoS2
> > monolayer. I optimized the system, did an scf and then tried to get
> Lowdin charges with projwcf. However, all charges are almost zero which is
> not
> > what I can expect:
> >
> > Lowdin Charges:
> >
> > Atom # 1: total charge = 0.0000, s = 0.0000,
> > Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px=
> 0.0000, py= 0.0000,
> > Atom # 2: total charge = 0.0001, s = 0.0000,
> > Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px=
> 0.0000, py= 0.0000,
> > Atom # 3: total charge = 0.0001, s = 0.0000,
> > Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px=
> 0.0000, py= 0.0000,
> > Atom # 4: total charge = 0.0000, s = 0.0000,
> > Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px=
> 0.0000, py= 0.0000,
> > Atom # 5: total charge = 0.0001, s = 0.0000,
> > Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px=
> 0.0000, py= 0.0000,
> > Atom # 6: total charge = 0.0001, s = 0.0000,
> > ....
> >
> > Could you please give me some advice of what I'm doing wrong?
> >
> > --------------------------------
> > The projwcf input:
> >
> > &PROJWFC
> > prefix = './3cell-cb_scf' ,
> > outdir = '.' ,
> > ngauss = 0.1 ,
> > DeltaE = 0.01 ,
> > /
> >
> > --------------------------------
> > The scf input:
> >
> > &CONTROL
> > calculation = 'scf' ,
> > restart_mode = 'from_scratch' ,
> > outdir = '.' ,
> > wfcdir = './tmp' ,
> > pseudo_dir = '.' ,
> > prefix = '3cell-cb_scf' ,
> > nstep = 1000 ,
> > tstress = .false. ,
> > /
> > &SYSTEM
> > ibrav = 4 ,
> > A = 9.495 ,
> > B = 9.495 ,
> > C = 100.0 ,
> > cosAB = 0.5 ,
> > cosAC = 0 ,
> > cosBC = 0 ,
> > nat = 39,
> > ntyp = 5,
> > ecutwfc = 35 ,
> > ecutrho = 140 ,
> > nosym = .true. ,
> > tot_charge = 0.000000 ,
> > /
> > &ELECTRONS
> > electron_maxstep = 200 ,
> > scf_must_converge = .false. ,
> > diagonalization='cg' ,
> > /
> > &IONS
> > ion_dynamics = 'bfgs' ,
> > /
> > ATOMIC_SPECIES
> > Mo 95.96 Mo_ONCV_PBE-1.0.upf
> > S 32.06 S_pbe_v1.2.uspp.F.UPF
> > C 12.011 C_pbe_v1.2.uspp.F.UPF
> > H 1.008 H.pbe-rrkjus_psl.0.1.UPF
> > Cl 35.45 cl_pbe_v1.4.uspp.F.UPF
> > ATOMIC_POSITIONS angstrom
> > Mo 1.392123361 1.675146760 5.927158394
> > S 1.409356288 3.492127081 4.353797199
> > S 1.409009361 3.492914431 7.500696022
> > Mo 2.974783806 4.416004278 5.927352435
> > S 2.991861295 6.232688291 4.353114990
> > S 2.991733615 6.233889787 7.500216780
> > Mo 4.557309411 7.156655993 5.926482117
> > S 4.574550104 8.974187415 4.353268832
> > S 4.573865790 8.974308816 7.499997172
> > Mo 4.556900653 1.675497042 5.926861427
> > S 4.573955171 3.492114510 4.352949498
> > S 4.574377417 3.492858021 7.500504130
> > Mo 6.139333906 4.416035304 5.926363713
> > S 6.156932316 6.232998289 4.352535948
> > S 6.156651090 6.233324282 7.500124138
> > Mo 7.721896396 7.156797182 5.926687354
> > S 7.739160210 8.974228888 4.353457824
> > S 7.739048493 8.974459743 7.500654977
> > Mo 7.722031044 1.675217921 5.926454615
> > S 7.739331052 3.492171149 4.352920557
> > S 7.738377057 3.492639347 7.499947690
> > Mo 9.304280720 4.416123626 5.927097215
> > S 9.321652087 6.232837357 4.353059451
> > S 9.321594176 6.234116854 7.500174405
> > Mo 10.887047440 7.156845127 5.926347019
> > S 10.903965611 8.974283787 4.353226240
> > S 10.903829602 8.974680010 7.500128022
> > C 5.700416780 4.960942076 11.705590151
> > C 5.786661978 6.354516349 11.705273773
> > C 7.046391983 6.956535202 11.705217371
> > C 8.203237318 6.173116561 11.705190411
> > C 8.099168585 4.780492709 11.705023203
> > C 6.846678887 4.164104064 11.704869934
> > Cl 4.129012811 4.204270654 11.705957792
> > H 4.877613854 6.955359406 11.704377918
> > H 7.118320846 8.046628444 11.704165169
> > H 9.184749419 6.647034640 11.704328004
> > H 8.998646725 4.161998637 11.704137157
> > H 6.757143341 3.077849963 11.704290956
> > K_POINTS automatic
> > 1 1 1 1 1 1
>
> ********************************************************
> - 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: 7
> Date: Fri, 24 Feb 2017 18:58:34 +0300
> From: Semen Yesylevskyy <yesint at mail.ru>
> Subject: Re: [Pw_forum] All Lowdin charges are zero
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1487951914.308180464 at f404.i.mail.ru>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Giuseppe,
> Thank you for quick reply, but I hardly understand the terms and local
> moonspeak because I'm using Quantum Espresso for few days only.
> I understand that some information for projwfc is missed but the topic you
> mentioned does not give me any clue of what should I do with my input to
> have it.
> Could you please point me to some step-by-step instruction of what should
> I do to get correct Lowdin charges? I googled for this extensively and the
> only thing which I've found is the following:
> 1) do optimization with pw.x
> 2) do scf with pw.x
> 3) run projwfc.x
>
> That is what I did without success...
>
> Sincerely,
> Dr. Semen Yesylevskyy
>
> Department of Physics of Biological Systems
> Institute of Physics of NAS of Ukraine
>
>
> >???????, 24 ??????? 2017, 17:44 +02:00 ?? Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it>:
> >
> >
> >
> >Dear Colleague (please sign always the posts with name and affiliation)
> >
> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the
> Hamann's code to include them.
> >Look for this old thread in the QE forum
> >
> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc
> >
> >That should contain all you need to rebuild a PP with wfcs and to obtain
> Lowdin charges with projwfc.x
> >
> >HTH
> >Giuseppe
> >
> >
> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:
> >> Dear All,
> >> I'm new to QE so please forgive if I'm missing something very obvious.
> I'm trying to study the charge transfer between organic molecules and MoS2
> >> monolayer. I optimized the system, did an scf and then tried to get
> Lowdin charges with projwcf. However, all charges are almost zero which is
> not
> >> what I can expect:
> >>
> >> Lowdin Charges:
> >>
> >> Atom # 1: total charge = 0.0000, s = 0.0000,
> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> Atom # 2: total charge = 0.0001, s = 0.0000,
> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> Atom # 3: total charge = 0.0001, s = 0.0000,
> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> Atom # 4: total charge = 0.0000, s = 0.0000,
> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> Atom # 5: total charge = 0.0001, s = 0.0000,
> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> Atom # 6: total charge = 0.0001, s = 0.0000,
> >> ....
> >>
> >> Could you please give me some advice of what I'm doing wrong?
> >>
> >> --------------------------------
> >> The projwcf input:
> >>
> >> &PROJWFC
> >> prefix = './3cell-cb_scf' ,
> >> outdir = '.' ,
> >> ngauss = 0.1 ,
> >> DeltaE = 0.01 ,
> >> /
> >>
> >> --------------------------------
> >> The scf input:
> >>
> >> &CONTROL
> >> calculation = 'scf' ,
> >> restart_mode = 'from_scratch' ,
> >> outdir = '.' ,
> >> wfcdir = './tmp' ,
> >> pseudo_dir = '.' ,
> >> prefix = '3cell-cb_scf' ,
> >> nstep = 1000 ,
> >> tstress = .false. ,
> >> /
> >> &SYSTEM
> >> ibrav = 4 ,
> >> A = 9.495 ,
> >> B = 9.495 ,
> >> C = 100.0 ,
> >> cosAB = 0.5 ,
> >> cosAC = 0 ,
> >> cosBC = 0 ,
> >> nat = 39,
> >> ntyp = 5,
> >> ecutwfc = 35 ,
> >> ecutrho = 140 ,
> >> nosym = .true. ,
> >> tot_charge = 0.000000 ,
> >> /
> >> &ELECTRONS
> >> electron_maxstep = 200 ,
> >> scf_must_converge = .false. ,
> >> diagonalization='cg' ,
> >> /
> >> &IONS
> >> ion_dynamics = 'bfgs' ,
> >> /
> >> ATOMIC_SPECIES
> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf
> >> S 32.06 S_pbe_v1.2.uspp.F.UPF
> >> C 12.011 C_pbe_v1.2.uspp.F.UPF
> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF
> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF
> >> ATOMIC_POSITIONS angstrom
> >> Mo 1.392123361 1.675146760 5.927158394
> >> S 1.409356288 3.492127081 4.353797199
> >> S 1.409009361 3.492914431 7.500696022
> >> Mo 2.974783806 4.416004278 5.927352435
> >> S 2.991861295 6.232688291 4.353114990
> >> S 2.991733615 6.233889787 7.500216780
> >> Mo 4.557309411 7.156655993 5.926482117
> >> S 4.574550104 8.974187415 4.353268832
> >> S 4.573865790 8.974308816 7.499997172
> >> Mo 4.556900653 1.675497042 5.926861427
> >> S 4.573955171 3.492114510 4.352949498
> >> S 4.574377417 3.492858021 7.500504130
> >> Mo 6.139333906 4.416035304 5.926363713
> >> S 6.156932316 6.232998289 4.352535948
> >> S 6.156651090 6.233324282 7.500124138
> >> Mo 7.721896396 7.156797182 5.926687354
> >> S 7.739160210 8.974228888 4.353457824
> >> S 7.739048493 8.974459743 7.500654977
> >> Mo 7.722031044 1.675217921 5.926454615
> >> S 7.739331052 3.492171149 4.352920557
> >> S 7.738377057 3.492639347 7.499947690
> >> Mo 9.304280720 4.416123626 5.927097215
> >> S 9.321652087 6.232837357 4.353059451
> >> S 9.321594176 6.234116854 7.500174405
> >> Mo 10.887047440 7.156845127 5.926347019
> >> S 10.903965611 8.974283787 4.353226240
> >> S 10.903829602 8.974680010 7.500128022
> >> C 5.700416780 4.960942076 11.705590151
> >> C 5.786661978 6.354516349 11.705273773
> >> C 7.046391983 6.956535202 11.705217371
> >> C 8.203237318 6.173116561 11.705190411
> >> C 8.099168585 4.780492709 11.705023203
> >> C 6.846678887 4.164104064 11.704869934
> >> Cl 4.129012811 4.204270654 11.705957792
> >> H 4.877613854 6.955359406 11.704377918
> >> H 7.118320846 8.046628444 11.704165169
> >> H 9.184749419 6.647034640 11.704328004
> >> H 8.998646725 4.161998637 11.704137157
> >> H 6.757143341 3.077849963 11.704290956
> >> K_POINTS automatic
> >> 1 1 1 1 1 1
> >
> >********************************************************
> >- 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
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
> a642b583/attachment-0001.html
>
> ------------------------------
>
> Message: 8
> Date: Fri, 24 Feb 2017 17:40:55 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Subject: Re: [Pw_forum] All Lowdin charges are zero
> To: pw_forum at pwscf.org
> Message-ID: <5515524.XkLPboe93X at amore2>
> Content-Type: text/plain; charset="ISO-8859-1"
>
>
> Dear Semen
> I suppose that you know what a pseudopotential is and how does it work...
> If you don't, I recommend first that you read this guide
> your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf
> and some of the references contained therein.
> Pseudopotentials can be generated by using the ld1.x (aka atomic) code
> embedded in the QE distributuin, but they are more often imported from
> various
> databases that are NOT part of the distribution, and are in such case used
> "at your own risk", even if there is a diffuse knowledge between QE users
> regarding the generation and usage of several kinds of pseudopotential.
>
> In your case, the optimized norm-conserving Vanderbilt's pseudopotentials
> (ONCV PPs) downloaded from this database
> http://www.quantum-simulation.org/potentials/sg15_oncv/
> do not contain the pseudowavefunctions, so projwfc.x does not find a
> suitable set of atomic orbitals to calculate the atomic projection of
> Kohn-Sham
> orbitals and the Lowdin partition of valence charge.
>
> If you want to use such PPs you should
>
> a) download and install the Hamann's code
>
> b) re-generate the same PPs by yourself with the input you find in the
> header at the beginning of the PP file
>
> And this was explained by Lorenzo Paulatto in the old thread mentioned in
> my previous mail.
>
> I suppose that it is not exactly easy for a newbie of PP generation, so
> for the time being I can only suggest you to use different
> pseudopotentials, or
> to try to find whether there is anybody who can do this work for you...:-)
> HTH
> Giuseppe
>
> On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote:
> > Dear Giuseppe,
> > Thank you for quick reply, but I hardly understand the terms and local
> moonspeak because I'm using Quantum Espresso for few days only.
> > I understand that some information for projwfc is missed but the topic
> you mentioned does not give me any clue of what should I do with my input to
> > have it. Could you please point me to some step-by-step instruction of
> what should I do to get correct Lowdin charges? I googled for this
> > extensively and the only thing which I've found is the following: 1) do
> optimization with pw.x
> > 2) do scf with pw.x
> > 3) run projwfc.x
> >
> > That is what I did without success...
> >
> > Sincerely,
> > Dr. Semen Yesylevskyy
> >
> > Department of Physics of Biological Systems
> > Institute of Physics of NAS of Ukraine
> >
> > >??????????????, 24 ?????????????? 2017, 17:44 +02:00 ???? Giuseppe
> Mattioli <giuseppe.mattioli at ism.cnr.it>:
> > >
> > >
> > >
> > >Dear Colleague (please sign always the posts with name and affiliation)
> > >
> > >ONCV PPs do not contain pseudowavefunctions, if you do not say to the
> Hamann's code to include them.
> > >Look for this old thread in the QE forum
> > >
> > >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc
> > >
> > >That should contain all you need to rebuild a PP with wfcs and to
> obtain Lowdin charges with projwfc.x
> > >
> > >HTH
> > >Giuseppe
> > >
> > >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:
> > >> Dear All,
> > >> I'm new to QE so please forgive if I'm missing something very
> obvious. I'm trying to study the charge transfer between organic molecules
> and MoS2
> > >> monolayer. I optimized the system, did an scf and then tried to get
> Lowdin charges with projwcf. However, all charges are almost zero which is
> > >> not
> > >> what I can expect:
> > >>
> > >> Lowdin Charges:
> > >> Atom # 1: total charge = 0.0000, s = 0.0000,
> > >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> > >> Atom # 2: total charge = 0.0001, s = 0.0000,
> > >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> > >> Atom # 3: total charge = 0.0001, s = 0.0000,
> > >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> > >> Atom # 4: total charge = 0.0000, s = 0.0000,
> > >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> > >> Atom # 5: total charge = 0.0001, s = 0.0000,
> > >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> > >> Atom # 6: total charge = 0.0001, s = 0.0000,
> > >>
> > >> ....
> > >>
> > >> Could you please give me some advice of what I'm doing wrong?
> > >>
> > >> --------------------------------
> > >>
> > >> The projwcf input:
> > >> &PROJWFC
> > >>
> > >> prefix = './3cell-cb_scf' ,
> > >> outdir = '.' ,
> > >> ngauss = 0.1 ,
> > >> DeltaE = 0.01 ,
> > >>
> > >> /
> > >>
> > >> --------------------------------
> > >>
> > >> The scf input:
> > >> &CONTROL
> > >>
> > >> calculation = 'scf' ,
> > >>
> > >> restart_mode = 'from_scratch' ,
> > >>
> > >> outdir = '.' ,
> > >> wfcdir = './tmp' ,
> > >>
> > >> pseudo_dir = '.' ,
> > >>
> > >> prefix = '3cell-cb_scf' ,
> > >>
> > >> nstep = 1000 ,
> > >>
> > >> tstress = .false. ,
> > >>
> > >> /
> > >> &SYSTEM
> > >>
> > >> ibrav = 4 ,
> > >>
> > >> A = 9.495 ,
> > >> B = 9.495 ,
> > >> C = 100.0 ,
> > >>
> > >> cosAB = 0.5 ,
> > >> cosAC = 0 ,
> > >> cosBC = 0 ,
> > >>
> > >> nat = 39,
> > >>
> > >> ntyp = 5,
> > >>
> > >> ecutwfc = 35 ,
> > >> ecutrho = 140 ,
> > >>
> > >> nosym = .true. ,
> > >>
> > >> tot_charge = 0.000000 ,
> > >>
> > >> /
> > >> &ELECTRONS
> > >>
> > >> electron_maxstep = 200 ,
> > >> scf_must_converge = .false. ,
> > >> diagonalization='cg' ,
> > >>
> > >> /
> > >> &IONS
> > >>
> > >> ion_dynamics = 'bfgs' ,
> > >>
> > >> /
> > >>
> > >> ATOMIC_SPECIES
> > >>
> > >> Mo 95.96 Mo_ONCV_PBE-1.0.upf
> > >>
> > >> S 32.06 S_pbe_v1.2.uspp.F.UPF
> > >> C 12.011 C_pbe_v1.2.uspp.F.UPF
> > >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF
> > >>
> > >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF
> > >>
> > >> ATOMIC_POSITIONS angstrom
> > >> Mo 1.392123361 1.675146760 5.927158394
> > >> S 1.409356288 3.492127081 4.353797199
> > >> S 1.409009361 3.492914431 7.500696022
> > >> Mo 2.974783806 4.416004278 5.927352435
> > >> S 2.991861295 6.232688291 4.353114990
> > >> S 2.991733615 6.233889787 7.500216780
> > >> Mo 4.557309411 7.156655993 5.926482117
> > >> S 4.574550104 8.974187415 4.353268832
> > >> S 4.573865790 8.974308816 7.499997172
> > >> Mo 4.556900653 1.675497042 5.926861427
> > >> S 4.573955171 3.492114510 4.352949498
> > >> S 4.574377417 3.492858021 7.500504130
> > >> Mo 6.139333906 4.416035304 5.926363713
> > >> S 6.156932316 6.232998289 4.352535948
> > >> S 6.156651090 6.233324282 7.500124138
> > >> Mo 7.721896396 7.156797182 5.926687354
> > >> S 7.739160210 8.974228888 4.353457824
> > >> S 7.739048493 8.974459743 7.500654977
> > >> Mo 7.722031044 1.675217921 5.926454615
> > >> S 7.739331052 3.492171149 4.352920557
> > >> S 7.738377057 3.492639347 7.499947690
> > >> Mo 9.304280720 4.416123626 5.927097215
> > >> S 9.321652087 6.232837357 4.353059451
> > >> S 9.321594176 6.234116854 7.500174405
> > >> Mo 10.887047440 7.156845127 5.926347019
> > >> S 10.903965611 8.974283787 4.353226240
> > >> S 10.903829602 8.974680010 7.500128022
> > >> C 5.700416780 4.960942076 11.705590151
> > >> C 5.786661978 6.354516349 11.705273773
> > >> C 7.046391983 6.956535202 11.705217371
> > >> C 8.203237318 6.173116561 11.705190411
> > >> C 8.099168585 4.780492709 11.705023203
> > >> C 6.846678887 4.164104064 11.704869934
> > >> Cl 4.129012811 4.204270654 11.705957792
> > >> H 4.877613854 6.955359406 11.704377918
> > >> H 7.118320846 8.046628444 11.704165169
> > >> H 9.184749419 6.647034640 11.704328004
> > >> H 8.998646725 4.161998637 11.704137157
> > >> H 6.757143341 3.077849963 11.704290956
> > >> K_POINTS automatic
> > >>
> > >> 1 1 1 1 1 1
> > >
> > >********************************************************
> > >- 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
>
> ********************************************************
> - 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: 9
> Date: Fri, 24 Feb 2017 22:24:09 +0530
> From: Sunetra Das <sunetra.das.88 at gmail.com>
> Subject: [Pw_forum] Error in routine phq_readin (5010)
> To: pw_forum at pwscf.org
> Message-ID:
> <CAPLukqnvyHp5vqp_eyeD-+jaF9J=GPWSDMd8VxeWeK57V5rqJg at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am trying to run the ph.x code for my system in espress0-5.0.3, but the
> code stops with the following error code:
>
>
>
>
>
>
> * %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> Error in routine phq_readin (5010): reading inputph
> namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%*
>
>
> Following is my input:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *phonon &INPUTPH outdir = './tmp'
> , prefix = 'In4' , ldisp =
> .true., dvscf_star%pat = .true. , recover
> = .false. , qplot = .false. ,
> q2d = .false. , q_in_band_form = .true. ,
> amass(1) = 114.82, iverbosity = 1,
> tr2_ph = 1e-10 , alpha_mix(1) = 0.7
> , nk1 = 31 , nk2 = 31
> , nk3 = 1 , k1 = 0
> , k2 = 0 , k3 = 0
> , nq1 = 5 , nq2 = 5
> , nq3 = 1 , /1.0 0.0 0.0 *
>
> Can anyone please help me with the above error message ?
> Thanks you.
>
> Sunetra.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://pwscf.org/pipermail/pw_forum/attachments/20170224/
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>
> ------------------------------
>
> Message: 10
> Date: Fri, 24 Feb 2017 20:12:20 +0300
> From: Semen Yesylevskyy <yesint at mail.ru>
> Subject: Re: [Pw_forum] All Lowdin charges are zero
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <1487956340.931890638 at f149.i.mail.ru>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Giuseppe,
> Thank you very much, now it is finally clear for me!
> Indeed I used PPs from "official" site. I had no idea that they may not
> contain some crucial pieces of information like wavefucntions.
> I really don't want to regenerate them at this stage because this work is
> a small side project which does not justify going so deep into the field.
> Are there any databases of pre-computed PPs with pseudowavefunctions
> included for H,C,Cl,S,Mo atoms?
>
> Sincerely,
> Semen
>
>
> >???????, 24 ??????? 2017, 18:40 +02:00 ?? Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it>:
> >
> >
> >Dear Semen
> >I suppose that you know what a pseudopotential is and how does it work...
> If you don't, I recommend first that you read this guide
> >your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf
> >and some of the references contained therein.
> >Pseudopotentials can be generated by using the ld1.x (aka atomic) code
> embedded in the QE distributuin, but they are more often imported from
> various
> >databases that are NOT part of the distribution, and are in such case
> used "at your own risk", even if there is a diffuse knowledge between QE
> users
> >regarding the generation and usage of several kinds of pseudopotential.
> >
> >In your case, the optimized norm-conserving Vanderbilt's pseudopotentials
> (ONCV PPs) downloaded from this database
> >http://www.quantum-simulation.org/potentials/sg15_oncv/
> >do not contain the pseudowavefunctions, so projwfc.x does not find a
> suitable set of atomic orbitals to calculate the atomic projection of
> Kohn-Sham
> >orbitals and the Lowdin partition of valence charge.
> >
> >If you want to use such PPs you should
> >
> >a) download and install the Hamann's code
> >
> >b) re-generate the same PPs by yourself with the input you find in the
> header at the beginning of the PP file
> >
> >And this was explained by Lorenzo Paulatto in the old thread mentioned in
> my previous mail.
> >?
> >I suppose that it is not exactly easy for a newbie of PP generation, so
> for the time being I can only suggest you to use different
> pseudopotentials, or
> >to try to find whether there is anybody who can do this work for you...:-)
> >HTH
> >Giuseppe
> >
> >On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote:
> >> Dear Giuseppe,
> >> Thank you for quick reply, but I hardly understand the terms and local
> moonspeak because I'm using Quantum Espresso for few days only.
> >> I understand that some information for projwfc is missed but the topic
> you mentioned does not give me any clue of what should I do with my input to
> >> have it. Could you please point me to some step-by-step instruction of
> what should I do to get correct Lowdin charges? I googled for this
> >> extensively and the only thing which I've found is the following: 1) do
> optimization with pw.x
> >> 2) do scf with pw.x
> >> 3) run projwfc.x
> >>
> >> That is what I did without success...
> >>
> >> Sincerely,
> >> Dr. Semen Yesylevskyy
> >>
> >> Department of Physics of Biological Systems
> >> Institute of Physics of NAS of Ukraine
> >>
> >> >??????????????, 24 ?????????????? 2017, 17:44 +02:00 ???? Giuseppe
> Mattioli < giuseppe.mattioli at ism.cnr.it >:
> >> >
> >> >
> >> >
> >> >Dear Colleague (please sign always the posts with name and affiliation)
> >> >
> >> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the
> Hamann's code to include them.
> >> >Look for this old thread in the QE forum
> >> >
> >> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc
> >> >
> >> >That should contain all you need to rebuild a PP with wfcs and to
> obtain Lowdin charges with projwfc.x
> >> >
> >> >HTH
> >> >Giuseppe
> >> >
> >> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:
> >> >> Dear All,
> >> >> I'm new to QE so please forgive if I'm missing something very
> obvious. I'm trying to study the charge transfer between organic molecules
> and MoS2
> >> >> monolayer. I optimized the system, did an scf and then tried to get
> Lowdin charges with projwcf. However, all charges are almost zero which is
> >> >> not
> >> >> what I can expect:
> >> >>
> >> >> Lowdin Charges:
> >> >> Atom # 1: total charge = 0.0000, s = 0.0000,
> >> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> >> Atom # 2: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> >> Atom # 3: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> >> Atom # 4: total charge = 0.0000, s = 0.0000,
> >> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> >> Atom # 5: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000,
> px= 0.0000, py= 0.0000,
> >> >> Atom # 6: total charge = 0.0001, s = 0.0000,
> >> >>
> >> >> ....
> >> >>
> >> >> Could you please give me some advice of what I'm doing wrong?
> >> >>
> >> >> --------------------------------
> >> >>
> >> >> The projwcf input:
> >> >> &PROJWFC
> >> >>
> >> >> prefix = './3cell-cb_scf' ,
> >> >> outdir = '.' ,
> >> >> ngauss = 0.1 ,
> >> >> DeltaE = 0.01 ,
> >> >>
> >> >> /
> >> >>
> >> >> --------------------------------
> >> >>
> >> >> The scf input:
> >> >> &CONTROL
> >> >>
> >> >> calculation = 'scf' ,
> >> >>
> >> >> restart_mode = 'from_scratch' ,
> >> >>
> >> >> outdir = '.' ,
> >> >> wfcdir = './tmp' ,
> >> >>
> >> >> pseudo_dir = '.' ,
> >> >>
> >> >> prefix = '3cell-cb_scf' ,
> >> >>
> >> >> nstep = 1000 ,
> >> >>
> >> >> tstress = .false. ,
> >> >>
> >> >> /
> >> >> &SYSTEM
> >> >>
> >> >> ibrav = 4 ,
> >> >>
> >> >> A = 9.495 ,
> >> >> B = 9.495 ,
> >> >> C = 100.0 ,
> >> >>
> >> >> cosAB = 0.5 ,
> >> >> cosAC = 0 ,
> >> >> cosBC = 0 ,
> >> >>
> >> >> nat = 39,
> >> >>
> >> >> ntyp = 5,
> >> >>
> >> >> ecutwfc = 35 ,
> >> >> ecutrho = 140 ,
> >> >>
> >> >> nosym = .true. ,
> >> >>
> >> >> tot_charge = 0.000000 ,
> >> >>
> >> >> /
> >> >> &ELECTRONS
> >> >>
> >> >> electron_maxstep = 200 ,
> >> >> scf_must_converge = .false. ,
> >> >> diagonalization='cg' ,
> >> >>
> >> >> /
> >> >> &IONS
> >> >>
> >> >> ion_dynamics = 'bfgs' ,
> >> >>
> >> >> /
> >> >>
> >> >> ATOMIC_SPECIES
> >> >>
> >> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf
> >> >>
> >> >> S 32.06 S_pbe_v1.2.uspp.F.UPF
> >> >> C 12.011 C_pbe_v1.2.uspp.F.UPF
> >> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF
> >> >>
> >> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF
> >> >>
> >> >> ATOMIC_POSITIONS angstrom
> >> >> Mo 1.392123361 1.675146760 5.927158394
> >> >> S 1.409356288 3.492127081 4.353797199
> >> >> S 1.409009361 3.492914431 7.500696022
> >> >> Mo 2.974783806 4.416004278 5.927352435
> >> >> S 2.991861295 6.232688291 4.353114990
> >> >> S 2.991733615 6.233889787 7.500216780
> >> >> Mo 4.557309411 7.156655993 5.926482117
> >> >> S 4.574550104 8.974187415 4.353268832
> >> >> S 4.573865790 8.974308816 7.499997172
> >> >> Mo 4.556900653 1.675497042 5.926861427
> >> >> S 4.573955171 3.492114510 4.352949498
> >> >> S 4.574377417 3.492858021 7.500504130
> >> >> Mo 6.139333906 4.416035304 5.926363713
> >> >> S 6.156932316 6.232998289 4.352535948
> >> >> S 6.156651090 6.233324282 7.500124138
> >> >> Mo 7.721896396 7.156797182 5.926687354
> >> >> S 7.739160210 8.974228888 4.353457824
> >> >> S 7.739048493 8.974459743 7.500654977
> >> >> Mo 7.722031044 1.675217921 5.926454615
> >> >> S 7.739331052 3.492171149 4.352920557
> >> >> S 7.738377057 3.492639347 7.499947690
> >> >> Mo 9.304280720 4.416123626 5.927097215
> >> >> S 9.321652087 6.232837357 4.353059451
> >> >> S 9.321594176 6.234116854 7.500174405
> >> >> Mo 10.887047440 7.156845127 5.926347019
> >> >> S 10.903965611 8.974283787 4.353226240
> >> >> S 10.903829602 8.974680010 7.500128022
> >> >> C 5.700416780 4.960942076 11.705590151
> >> >> C 5.786661978 6.354516349 11.705273773
> >> >> C 7.046391983 6.956535202 11.705217371
> >> >> C 8.203237318 6.173116561 11.705190411
> >> >> C 8.099168585 4.780492709 11.705023203
> >> >> C 6.846678887 4.164104064 11.704869934
> >> >> Cl 4.129012811 4.204270654 11.705957792
> >> >> H 4.877613854 6.955359406 11.704377918
> >> >> H 7.118320846 8.046628444 11.704165169
> >> >> H 9.184749419 6.647034640 11.704328004
> >> >> H 8.998646725 4.161998637 11.704137157
> >> >> H 6.757143341 3.077849963 11.704290956
> >> >> K_POINTS automatic
> >> >>
> >> >> 1 1 1 1 1 1
> >> >
> >> >********************************************************
> >> >- 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
> >
> >********************************************************
> >- 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
>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 11
> Date: Fri, 24 Feb 2017 17:52:12 +0000
> From: Louis Fry-Bouriaux <ellf at leeds.ac.uk>
> Subject: Re: [Pw_forum] Error in routine phq_readin (5010)
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID:
> <DB5PR0301MB1942C6C26EFCC7F825E5EC649E520 at DB5PR0301MB1942.
> eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Sunetra,
>
>
> It might be the comma on the last parameter, with certain namelists
> this causes a parsing error. I haven't tested though but try remove that
> last comma:
>
>
> nq2 = 5 ,
> nq3 = 1 <------------
> /
> 1.0 0.0 0.0
>
>
> If that doesn't work other input fields might not be correct..
>
>
> Kindest regards,
>
> Louis
>
> ________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
> of Sunetra Das <sunetra.das.88 at gmail.com>
> Sent: 24 February 2017 16:54:09
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] Error in routine phq_readin (5010)
>
> Hello all,
>
> I am trying to run the ph.x code for my system in espress0-5.0.3, but the
> code stops with the following error code:
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
> Error in routine phq_readin (5010):
> reading inputph namelist
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%%%%%%%%%%%%%%%
>
>
> Following is my input:
>
> phonon
> &INPUTPH
> outdir = './tmp' ,
> prefix = 'In4' ,
> ldisp = .true.,
> dvscf_star%pat = .true. ,
> recover = .false. ,
> qplot = .false. ,
> q2d = .false. ,
> q_in_band_form = .true. ,
> amass(1) = 114.82,
> iverbosity = 1,
> tr2_ph = 1e-10 ,
> alpha_mix(1) = 0.7 ,
> nk1 = 31 ,
> nk2 = 31 ,
> nk3 = 1 ,
> k1 = 0 ,
> k2 = 0 ,
> k3 = 0 ,
> nq1 = 5 ,
> nq2 = 5 ,
> nq3 = 1 ,
> /
> 1.0 0.0 0.0
>
>
> Can anyone please help me with the above error message ?
> Thanks you.
>
> Sunetra.
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 12
> Date: Fri, 24 Feb 2017 19:03:59 +0100 (CET)
> From: Andrea Ferretti <andrea.ferretti at unimore.it>
> Subject: [Pw_forum] MaX user portal and newsletter
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <alpine.DEB.2.10.1702241902410.11726 at potzie>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
>
>
>
> Dear All,
>
> this email is to inform that the MaX user portal, offering services also
> connected to Quantum ESPRESSO and its community, is now ready. Everyone can
> subscribe. For further information please have a look at the MaX
> newsletter
> (link below).
>
> take care
> Andrea
>
> ==================================
>
> MaX User Portal ready
>
> Six services are now up and r...
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