Thank you for your help, Mr. Jing Yang. On 24 February 2017 at 16:30, <[email protected]> wrote:
> Send Pw_forum mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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 <[email protected]> > Subject: Re: [Pw_forum] Silicon 111 surface > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > 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 < > [email protected]> 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 <[email protected] <mailto: > [email protected]>> 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 > >>> [email protected] <mailto:[email protected]> > >>> 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: [email protected] <mailto:giovanni.cantele@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 > >> [email protected] > >> 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: [email protected] > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.na.infn.it/~cantele > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170223/ > f36ab261/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Thu, 23 Feb 2017 12:42:04 +0000 > From: Louis Fry-Bouriaux <[email protected]> > Subject: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino > example > To: "[email protected]" <[email protected]> > Message-ID: > <DB5PR0301MB1942FC78116BD10A9A9B72C49E530@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 -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170223/ > 770d37e0/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Thu, 23 Feb 2017 19:02:05 +0000 > From: Louis Fry-Bouriaux <[email protected]> > Subject: Re: [Pw_forum] Symmetry recognition > To: PWSCF Forum <[email protected]> > Message-ID: > <DB5PR0301MB1942D7D22B680834994E9D779E530@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: [email protected] <[email protected]> on behalf > of Pascal Boulet <[email protected]> > 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 : > [email protected]<mailto:[email protected]> > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170223/ > 4f55c86c/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Thu, 23 Feb 2017 21:04:21 +0100 > From: Paolo Giannozzi <[email protected]> > Subject: Re: [Pw_forum] Symmetry recognition > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCtz160Sd8rySjBC67s2SHhTOcmNViZ3=RJLjzL8-z6LTQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Thu, Feb 23, 2017 at 8:02 PM, Louis Fry-Bouriaux <[email protected]> > 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/ > 75ee9fcb/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Thu, 23 Feb 2017 20:12:52 +0000 > From: Louis Fry-Bouriaux <[email protected]> > Subject: Re: [Pw_forum] Symmetry recognition > To: PWSCF Forum <[email protected]> > Message-ID: > <DB5PR0301MB19424D8B5FDB86E577B109189E530@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: [email protected] <[email protected]> on behalf > of Paolo Giannozzi <[email protected]> > 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 <[email protected] > <mailto:[email protected]>> 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 <[email protected]> > Subject: Re: [Pw_forum] Symmetry recognition > To: PWSCF Forum <[email protected]> > Message-ID: > <CAPMgbCtiYOpZxFHY0H+-xFJb2c=a+5dM15xO0C_LB4LRH4+uqw@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 > <[email protected]> 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 : > > [email protected] > > > > > > > > > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > 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 <[email protected]> > Subject: [Pw_forum] (no subject) > To: [email protected] > Message-ID: > <CAPLukqnb5yf+k8-EmkMwitWeiGZcx_PrasB1MRigfGyRwBe9Sg@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 <[email protected]> > Subject: [Pw_forum] Charge is wrong error > To: [email protected] > Message-ID: > <CAPLukqm1kSk-VFg7eMjJGPmHVeZfUwK=0qZW+ > [email protected]> > 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 <[email protected]> > Subject: Re: [Pw_forum] Charge is wrong error > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > 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 <[email protected]> > 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 > > [email protected] > > 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 <[email protected]> > Subject: [Pw_forum] basis set module PROJWFC > To: [email protected] > Message-ID: > <CAJKZiECH-kcJkiyC_TNxKUTsdLknfKHCgS2P9Zssy+ > [email protected]> > 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 <[email protected]> > Subject: Re: [Pw_forum] About output of PDOS calculations of CeO2 > To: [email protected] > Message-ID: <36291620.ELma9kdhud@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 <[email protected]> > > > > 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 > > > > > > <[email protected]> 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 < > > > >> > > > >> [email protected]> 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 > > > >> > [email protected] > > > >> > 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: <[email protected]> > > > > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > > > > ResearcherID: F-6308-2012 > > > > > > > > _______________________________________________ > > > > Pw_forum mailing list > > > > [email protected] > > > > 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 > > > [email protected] > > > 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: <[email protected]> > 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 <[email protected]> > Subject: Re: [Pw_forum] basis set module PROJWFC > To: PWSCF Forum <[email protected]> > Message-ID: <1966835.skiQF9jZZP@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 > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 115, Issue 24 > ***************************************** > >
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