<p dir="ltr">Hello for all<br>
so l need the in put of TiO2 ( bluk)<br>
Thanks</p>
<div class="gmail_quote">بتاريخ ٢٥/٠٢/٢٠١٧ ٢:٠٠ م، جاء من <<a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a>>:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Topic 8 (Sunetra Das)<br>
2. Re: ESM Example (Al slab with bc2) and Otani/Sugino example<br>
(Minoru Otani)<br>
3. Re: Symmetry recognition (Pascal Boulet)<br>
4. Re: ESM Example (Al slab with bc2) and Otani/Sugino example<br>
(Louis Fry-Bouriaux)<br>
5. All Lowdin charges are zero (Semen Yesylevskyy)<br>
6. Re: All Lowdin charges are zero (Giuseppe Mattioli)<br>
7. Re: All Lowdin charges are zero (Semen Yesylevskyy)<br>
8. Re: All Lowdin charges are zero (Giuseppe Mattioli)<br>
9. Error in routine phq_readin (5010) (Sunetra Das)<br>
10. Re: All Lowdin charges are zero (Semen Yesylevskyy)<br>
11. Re: Error in routine phq_readin (5010) (Louis Fry-Bouriaux)<br>
12. MaX user portal and newsletter (Andrea Ferretti)<br>
13. Re: Error in routine phq_readin (5010) (Paolo Giannozzi)<br>
14. Re: Error in routine phq_readin (5010) (dario rocca)<br>
15. Re: Error in routine phq_readin (5010) (Louis Fry-Bouriaux)<br>
16. Re: Error in routine phq_readin (5010) (Lorenzo Paulatto)<br>
17. MaX user portal and newsletter (fwd) (Andrea Ferretti)<br>
18. The unit of potential (??)<br>
<br>
<br>
------------------------------<wbr>------------------------------<wbr>----------<br>
<br>
Message: 1<br>
Date: Fri, 24 Feb 2017 18:20:31 +0530<br>
From: Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
Subject: Re: [Pw_forum] Topic 8<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAPLukqmjD6jr4U4ZOZ6Q_RBvpVMcAvuf1GzY4NR6DgnkqvA_RQ@mail.gmail.com">CAPLukqmjD6jr4U4ZOZ6Q_<wbr>RBvpVMcAvuf1GzY4NR6DgnkqvA_RQ@<wbr>mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Thank you for your help, Mr. Jing Yang.<br>
<br>
On 24 February 2017 at 16:30, <<a href="mailto:pw_forum-request@pwscf.org">pw_forum-request@pwscf.org</a>> wrote:<br>
<br>
> Send Pw_forum mailing list submissions to<br>
> <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
><br>
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> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
> or, via email, send a message with subject or body 'help' to<br>
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><br>
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><br>
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> Today's Topics:<br>
><br>
> 1. Re: Silicon 111 surface (Giovanni Cantele)<br>
> 2. ESM Example (Al slab with bc2) and Otani/Sugino example<br>
> (Louis Fry-Bouriaux)<br>
> 3. Re: Symmetry recognition (Louis Fry-Bouriaux)<br>
> 4. Re: Symmetry recognition (Paolo Giannozzi)<br>
> 5. Re: Symmetry recognition (Louis Fry-Bouriaux)<br>
> 6. Re: Symmetry recognition (Paolo Giannozzi)<br>
> 7. (no subject) (Sunetra Das)<br>
> 8. Charge is wrong error (Sunetra Das)<br>
> 9. Re: Charge is wrong error (Jing Yang)<br>
> 10. basis set module PROJWFC (alberto)<br>
> 11. Re: About output of PDOS calculations of CeO2 (Giuseppe Mattioli)<br>
> 12. Re: basis set module PROJWFC (Lorenzo Paulatto)<br>
><br>
><br>
> ------------------------------<wbr>------------------------------<wbr>----------<br>
><br>
> Message: 1<br>
> Date: Thu, 23 Feb 2017 12:19:23 +0100<br>
> From: Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a>><br>
> Subject: Re: [Pw_forum] Silicon 111 surface<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID: <<a href="mailto:46431764-885C-414F-8833-8087FE3E2308@spin.cnr.it">46431764-885C-414F-8833-<wbr>8087FE3E2308@spin.cnr.it</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi,<br>
> this is the reply to the message you sent me, it is better for me to<br>
> continue di discussion on PW_forum, being a way<br>
> to share doubts, mistakes, problems with many other people that might help!<br>
><br>
> You can build your Si(111) surface with any tool (by hand, using VNL, any<br>
> other builder), but this tool will do just what<br>
> you ask it to do, so before using the tool you ALWAYS need basic<br>
> understanding. In this respect, I also suggest to look<br>
> to the extensive documentation of Quantum-ESPRESSO and to the tutorials<br>
> that are freely available in the web.<br>
><br>
> Coming to your problem, Quantum-ESPRESSO, as you know, is based on plane<br>
> waves, as such can only handle<br>
> systems that are periodic in all three directions. If you need to simulate<br>
> something that is periodic in only two, one or no<br>
> direction in space (a surface, a 1D wire, a cluster/molecule/quantum dot<br>
> respectively) you use the supercell approach.<br>
><br>
> Let?s consider the case of a surface and let?s choose x and y as<br>
> directions parallel to the surface, such that the z direction is orthogonal<br>
> to it (you can make a different choice, of course).<br>
><br>
> 1) In the x-y plane you have to identify the surface unit cell, spanned by<br>
> two vectors a1 and a2 that describe the surface periodicity.<br>
> Beware the choice of a1 and a2: they might be deduced from the bulk<br>
> crystals or be more complicated if the surface<br>
> is along special directions or if it undergoes some reconstruction.<br>
><br>
> In the case of Si(111) you should first decide if you want to choose the<br>
> minimal cell, or if you want to consider complex reconstruction<br>
> (that is structures where one or more surface unit cells are gathered to<br>
> build more complex structures) The minimal cell is obtained<br>
> by considering the 111 plane of Si and trying to understand the<br>
> periodicity vectors within that plane. The complex reconstruction are<br>
> instead<br>
> obtained once you know how many cells are gathered along the a1 and a2<br>
> directions. For example, in the case of Si(111), whose structure<br>
> had been long debated many years ago, it can undergo a 7x7 reconstruction<br>
> (with a very large surface unit cell). You can find details wherever,<br>
> for example this is one of the Google search results:<br>
> <a href="http://nanowiz.tripod.com/sisteps/si111.htm" rel="noreferrer" target="_blank">http://nanowiz.tripod.com/<wbr>sisteps/si111.htm</a> <<a href="http://nanowiz.tripod.com/" rel="noreferrer" target="_blank">http://nanowiz.tripod.com/</a><br>
> sisteps/si111.htm><br>
><br>
><br>
> 2) once the surface unit cell is identified, you must decide how many<br>
> planes you want to consider in the direction (z-axis) orthogonal to the<br>
> surface.<br>
> In this case beware the fact that as you move in along z, you might meet<br>
> one or more planes that are not equivalent to the 1st one. In other words,<br>
> the second plane might not be obtained simply through a rigid shift along<br>
> z of the 1st one, but there might be 2 or more planes before one equivalent<br>
> to the first one is found<br>
><br>
><br>
> 3) at this point you have the minimal number of atomic coordinates that,<br>
> replicated along a1 and a2 reproduce a slab, that is, a Si(111) surface<br>
> composed<br>
> by a certain number of planes. How to choose a3 (this is one of the issues<br>
> in your input file)? You measure the distance d along the z axis between<br>
> the two furthermost planes<br>
> AND and set the length of a3 to d+V, where V=vacuum space. The latter is<br>
> needed because, in the supercell approach, you system is replicated<br>
> also along a3, but you don?t want that periodic replicas interact with<br>
> each other. The amount of V, let?s say 10 A (but a larger value might be<br>
> needed), is chosen<br>
> just to avoid interaction and convergence with respect to it must always<br>
> be checked<br>
><br>
><br>
> 4) because the z direction is not a true periodicity direction, if V is<br>
> large enough you expect that the band dispersion is zero along the z<br>
> direction, that is,<br>
> you should obtain flat bands along that direction. As such, Brillouin zone<br>
> sampling along that direction is useless, and the k-point grid you use for<br>
> scf/relax<br>
> calculations is in the form N x M x 1<br>
><br>
><br>
> Whether you performs steps 1-4 by hand or using some tool such as VNL is<br>
> up to you. I suggest to start with simple surfaces and simple crystals, to<br>
> start with.<br>
><br>
> Giovanni<br>
><br>
> PS after writing this message, I have tried the Google search<br>
> build surface supercell Quantum-ESPRESSO<br>
> The 1st result is this link (I?m sure that many many others of interest<br>
> for you show up!)<br>
> <a href="http://www.democritos.it/events/pw-tutorial/lectures/pw-tutorial.pdf" rel="noreferrer" target="_blank">http://www.democritos.it/<wbr>events/pw-tutorial/lectures/<wbr>pw-tutorial.pdf</a><br>
> If I were you, I would start with the exercises described therein.<br>
><br>
> > Actually sir I am trying to create a silicon 111 surface adsorbed by an<br>
> Indium atom.To do this what should I be do first? The input file which I am<br>
> using is create by the VNL GUI. Is there any other way to create a quantum<br>
> espresso input file.<br>
> > Thanx<br>
> ><br>
> ><br>
> >> On 23 Feb 2017, at 10:18, Giovanni Cantele <<br>
> <a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a>> wrote:<br>
> >><br>
> >> 1) the atomic positions are likely wrong, I cannot understand what is<br>
> the system you want to calculate. For example, the Si-In distance is 1.1 A,<br>
> that looks<br>
> >> very small. Try to look at your structure, opening the input file with<br>
> XCrysDen. It is worth, before performing any further calculation, to check<br>
> whether it is EXACTLY what you want.<br>
> >><br>
> >><br>
> >> 2) in the case you would like to simulate the Si(111) SURFACE in the<br>
> presence of In, your input does not correspond to a surface calculation.<br>
> There is not vacuum space<br>
> >> introduced between periodic replicas of the same slab, and there is<br>
> k-point sampling in the direction orthogonal to the surface. If instead you<br>
> are studying something like<br>
> >> a Si heterostructure (e.g. a superlattice), please disregard this point<br>
> >><br>
> >> 3) you are using ultra soft pseudo potential, the ecutwfc is likely too<br>
> high (this however does not give convergence issues, but can make your<br>
> calculation much slower<br>
> >> than needed!). On the other hand, you are not setting the ecutrho<br>
> variable, that by default is 4*ecutwfc. For ultrasoft pseudo potentials, as<br>
> you might learn reading<br>
> >> the relevant literature on the subject, a higher charge density cut-off<br>
> is required, usually from 6 to 12 times ecutwfc<br>
> >><br>
> >> 4) to improve convergence, increasing degauss might help, for systems<br>
> very difficult to converge (but even in this case you should be aware of<br>
> what degauss is and how to use it)<br>
> >> and also decrease mixing_beta to 0.3, or 0.1 or maybe even less<br>
> >><br>
> >><br>
> >> Giovanni<br>
> >><br>
> >><br>
> >><br>
> >>> On 23 Feb 2017, at 06:59, Ubaid Mohd <<a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a> <mailto:<br>
> <a href="mailto:onlymubaid@gmail.com">onlymubaid@gmail.com</a>>> wrote:<br>
> >>><br>
> >>> Hi,<br>
> >>><br>
> >>> I am trying to scf calculation of silicon(111)_Indium and the total<br>
> force on the atom is not converging. Initially, the scf cycle itself was<br>
> not converging.<br>
> >>> What is wron with my input file.<br>
> >>> Thanx,<br>
> >>> Ubaid<br>
> >>><br>
> >>><br>
> >>><br>
> >>><br>
> >>> Input File<br>
> >>><br>
> >>><br>
> >>> &CONTROL<br>
> >>> calculation='scf',<br>
> >>> outdir='Pwscf',<br>
> >>> prefix='Si_In',<br>
> >>> pseudo_dir='.',<br>
> >>> verbosity='low',<br>
> >>> /<br>
> >>><br>
> >>> &SYSTEM<br>
> >>> ibrav=0,<br>
> >>> celldm(1)=7.2565749368d0,<br>
> >>> nat=7,<br>
> >>> ntyp=2,<br>
> >>> ecutwfc=90,<br>
> >>> input_dft='PBE',<br>
> >>> occupations='smearing',<br>
> >>> smearing='mv',<br>
> >>> degauss=0.005d0,<br>
> >>> /<br>
> >>><br>
> >>> &ELECTRONS<br>
> >>> conv_thr=1d-06,<br>
> >>> mixing_beta=0.7d0,<br>
> >>> /<br>
> >>><br>
> >>> ATOMIC_SPECIES<br>
> >>> In 114.818000d0 In.pbe-d-rrkjus.UPF<br>
> >>> Si 28.085500d0 Si.pbe-n-rrkjus_psl.0.1.UPF<br>
> >>><br>
> >>> ATOMIC_POSITIONS {crystal}<br>
> >>> Si 0.1708493746d0 0.3787081237d0 0.2302895286d0<br>
> >>> Si 0.8375160412d0 0.7120414570d0 0.3136228619d0<br>
> >>> Si 0.8375160412d0 0.7120414570d0 0.5636228619d0<br>
> >>> Si 0.5041827079d0 1.0453747903d0 0.6469561953d0<br>
> >>> Si 0.5041827079d0 1.0453747903d0 0.8969561953d0<br>
> >>> Si 0.1708493746d0 0.3787081237d0 0.9802895286d0<br>
> >>> In 0.2708493746d0 0.4787081237d0 0.3397104714d0<br>
> >>><br>
> >>> K_POINTS {automatic}<br>
> >>> 5 5 5 0 0 0<br>
> >>><br>
> >>> CELL_PARAMETERS {alat}<br>
> >>> 1.000000000000d0 0.000000000000d0 0.000000000000d0<br>
> >>> -0.500000000000d0 0.866025403784d0 0.000000000000d0<br>
> >>> 0.000000000000d0 0.000000000000d0 2.449489742783d0<br>
> >>><br>
> >>><br>
> >>> ______________________________<wbr>_________________<br>
> >>> Pw_forum mailing list<br>
> >>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a> <mailto:<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>><br>
> >>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
> >><br>
> >> --<br>
> >><br>
> >> Giovanni Cantele, PhD<br>
> >> CNR-SPIN<br>
> >> c/o Dipartimento di Fisica<br>
> >> Universita' di Napoli "Federico II"<br>
> >> Complesso Universitario M. S. Angelo - Ed. 6<br>
> >> Via Cintia, I-80126, Napoli, Italy<br>
> >> e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a> <mailto:<a href="mailto:giovanni.cantele@spin">giovanni.cantele@spin</a>.<br>
> <a href="http://cnr.it" rel="noreferrer" target="_blank">cnr.it</a>><br>
> >> Phone: +39 081 676910<br>
> >> Skype contact: giocan74<br>
> >><br>
> >> ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/<wbr>rid/A-1951-2009</a> <<br>
> <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/<wbr>rid/A-1951-2009</a>><br>
> >> Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~<wbr>cantele</a> <<a href="http://people.na.infn.it/~" rel="noreferrer" target="_blank">http://people.na.infn.it/~</a><br>
> cantele><br>
> >><br>
> >> ______________________________<wbr>_________________<br>
> >> Pw_forum mailing list<br>
> >> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> >> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
><br>
> --<br>
><br>
> Giovanni Cantele, PhD<br>
> CNR-SPIN<br>
> c/o Dipartimento di Fisica<br>
> Universita' di Napoli "Federico II"<br>
> Complesso Universitario M. S. Angelo - Ed. 6<br>
> Via Cintia, I-80126, Napoli, Italy<br>
> e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it">giovanni.cantele@spin.cnr.it</a><br>
> Phone: +39 081 676910<br>
> Skype contact: giocan74<br>
><br>
> ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/<wbr>rid/A-1951-2009</a><br>
> Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~<wbr>cantele</a><br>
><br>
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> f36ab261/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Thu, 23 Feb 2017 12:42:04 +0000<br>
> From: Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
> Subject: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino<br>
> example<br>
> To: "<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<wbr>DB5PR0301MB1942FC78116BD10A9A9<wbr>B72C49E530@DB5PR0301MB1942.<br>
> <a href="http://eurprd03.prod.outlook.com" rel="noreferrer" target="_blank">eurprd03.prod.outlook.com</a>><br>
><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Hi there,<br>
><br>
><br>
> I am trying to understand the ESM example with bc2 (metal-slab-metal)<br>
> distributed with QE 6.0 which consists of an Al(001) slab between two<br>
> electrodes, and at the same time I am trying to replicate the results of<br>
> Otani and Sugino in their paper (Phys. Rev. B, 73, 115407, 2006) which<br>
> consists of an Al/Si(111)/Al slab between two screening boundaries.<br>
><br>
><br>
> I have a few questions:<br>
><br>
><br>
> ** 1. ** In the QE example the following cell params and atomic positions<br>
> are specified:<br>
><br>
><br>
> CELL_PARAMETERS bohr<br>
> 10.82227686 0.00000000 0.00000000<br>
> 0.00000000 10.82227686 0.00000000<br>
> 0.00000000 0.00000000 22.67672253<br>
> ATOMIC_POSITIONS bohr<br>
> Al 0.00000000 0.00000000 0.00000000<br>
> Al 5.41113843 0.00000000 0.00000000<br>
> Al 0.00000000 5.41113843 0.00000000<br>
> Al 5.41113843 5.41113843 0.00000000<br>
><br>
><br>
> My understanding is that the cell will repeat without overlapping atoms<br>
> along X and Y. What I'm not clear on is why the 3rd lattice vector is so<br>
> large?<br>
><br>
><br>
> The parameter 'esm_w' defaults to zero and is not specified in the<br>
> example, so does this large value mean that there is a region of vacuum? Or<br>
> does it just repeat the atoms such that in the Z-direction there are 5 Al<br>
> layers? I'm guessing that this 3rd cell parameter Z-value corresponds to<br>
> L_z, which in the paper corresponds to z_0?<br>
><br>
><br>
> ** 2. ** I have reproduced the 'surface unit cell' from Otani/Sugino's<br>
> paper using VESTA.<br>
><br>
><br>
> My concern here is with the correct repetition of atoms in X and Y, and<br>
> what exactly happens with the Z direction. I realize I must first rotate<br>
> the unit cell such that the repeated Al atoms lie perpendicular to the Z<br>
> Cartesian axis which I have not done yet.<br>
><br>
><br>
> I have tested the repetition of this cell within VESTA along vectors<br>
> perpendicular to the Al plane. So my most important question is: if the<br>
> height of the cell along Z is ~14.4281 Angstrom (measured from Al center<br>
> plane), then the third 'CELL_PARAMETERS' entry (after rotation) should be<br>
> this value exactly + the 'decay length' of the wavefunction in Z? Then the<br>
> parameter 'esm_w' is used to set z_1 from the paper I suppose?<br>
><br>
><br>
> I will generate an xyz file of the surface cell, but if I repeat by 3.816<br>
> A along a surface lattice vector, it is a matter of just deleting the<br>
> entries that cause an overlap of the atoms I suppose?<br>
><br>
><br>
> Thank you for your time and sorry for the very long email,<br>
><br>
> Kindest regards,<br>
><br>
> Louis<br>
><br>
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> 770d37e0/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Thu, 23 Feb 2017 19:02:05 +0000<br>
> From: Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
> Subject: Re: [Pw_forum] Symmetry recognition<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<wbr>DB5PR0301MB1942D7D22B680834994<wbr>E9D779E530@DB5PR0301MB1942.<br>
> <a href="http://eurprd03.prod.outlook.com" rel="noreferrer" target="_blank">eurprd03.prod.outlook.com</a>><br>
><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Hi Pascal,<br>
><br>
><br>
> When I first started using QE 6.0 not long ago I had trouble using<br>
> crystal_sg, I suppose you have the Wyckoff positions of your atoms. What I<br>
> did was use the VESTA program which allows you to input Wyckoff positions<br>
> and it will correctly generate the cell as long as other options are<br>
> correct. I then exported to an xyz file and converted the coordinates in<br>
> angstroms to internal crystal coordinates ('crystal' option) using:<br>
><br>
> <a href="https://en.wikipedia.org/wiki/Fractional_coordinates" rel="noreferrer" target="_blank">https://en.wikipedia.org/wiki/<wbr>Fractional_coordinates</a><br>
><br>
> Fractional coordinates - Wikipedia<<a href="https://en" rel="noreferrer" target="_blank">https://en</a>.<br>
> <a href="http://wikipedia.org/wiki/Fractional_coordinates" rel="noreferrer" target="_blank">wikipedia.org/wiki/Fractional_<wbr>coordinates</a>><br>
> <a href="http://en.wikipedia.org" rel="noreferrer" target="_blank">en.wikipedia.org</a><br>
> In crystallography, a fractional coordinate system is a coordinate system<br>
> in which the edges of the unit cell are used as the basic vectors to<br>
> describe the positions ...<br>
><br>
><br>
> Which worked perfectly for me. This is easily done with a Python script or<br>
> something similar!<br>
><br>
><br>
> Kindest regards,<br>
><br>
> Louis<br>
><br>
> ______________________________<wbr>__<br>
> From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on behalf<br>
> of Pascal Boulet <<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>><br>
> Sent: 23 February 2017 07:56:16<br>
> To: PWSCF Forum<br>
> Subject: [Pw_forum] Symmetry recognition<br>
><br>
> Dear all,<br>
><br>
> I am running a structural optimization with QE 6.0. The structure is<br>
> orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not<br>
> converge so I have to restart it. But as I restart it, the number of<br>
> symmetry is now 4, there is a descent of symmetry. I shall say that I use<br>
> the space_group option with COORDINATES crystal_sg. But the problem remains<br>
> if I put all the coordinates (unsurprisingly).<br>
><br>
> Is there a reason for this, and can I avoid this?<br>
><br>
> Thank you<br>
> Best regards<br>
> Pascal<br>
><br>
> -<br>
> Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE<br>
> Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie Niemen<br>
> - 13013 Marseille<br>
> T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50<br>
> Site : <a href="http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire" rel="noreferrer" target="_blank">http://madirel.univ-amu.fr/<wbr>pages_web_BOULET_PASCAL/<wbr>annuaire</a><<br>
> <a href="http://amu.fr/pages_web_BOULET_PASCAL/annuaire" rel="noreferrer" target="_blank">http://amu.fr/pages_web_<wbr>BOULET_PASCAL/annuaire</a>> - Email :<br>
> <a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a><<wbr>mailto:<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.<wbr>fr</a>><br>
><br>
><br>
><br>
><br>
> -------------- next part --------------<br>
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> 4f55c86c/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 4<br>
> Date: Thu, 23 Feb 2017 21:04:21 +0100<br>
> From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
> Subject: Re: [Pw_forum] Symmetry recognition<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<wbr>CAPMgbCtz160Sd8rySjBC67s2SHhTO<wbr>cmNViZ3=RJLjzL8-z6LTQ@mail.<br>
> <a href="http://gmail.com" rel="noreferrer" target="_blank">gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> On Thu, Feb 23, 2017 at 8:02 PM, Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
> wrote:<br>
><br>
> When I first started using QE 6.0 not long ago I had trouble using<br>
> > crystal_sg<br>
> ><br>
><br>
> Why?<br>
> -------------- next part --------------<br>
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> 75ee9fcb/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 5<br>
> Date: Thu, 23 Feb 2017 20:12:52 +0000<br>
> From: Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
> Subject: Re: [Pw_forum] Symmetry recognition<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <<wbr>DB5PR0301MB19424D8B5FDB86E577B<wbr>109189E530@DB5PR0301MB1942.<br>
> <a href="http://eurprd03.prod.outlook.com" rel="noreferrer" target="_blank">eurprd03.prod.outlook.com</a>><br>
><br>
> Content-Type: text/plain; charset="us-ascii"<br>
><br>
> Hey Paolo,<br>
><br>
><br>
> I gave up as it wouldn't parse the input I provided, it was definitely<br>
> my fault, so I gave up and used the method I described which worked fine. I<br>
> didn't mean to imply there was a problem with the software, sorry about<br>
> that.<br>
><br>
><br>
> Louis<br>
><br>
> ______________________________<wbr>__<br>
> From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on behalf<br>
> of Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
> Sent: 23 February 2017 20:04:21<br>
> To: PWSCF Forum<br>
> Subject: Re: [Pw_forum] Symmetry recognition<br>
><br>
> On Thu, Feb 23, 2017 at 8:02 PM, Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a><br>
> <mailto:<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>>> wrote:<br>
><br>
> When I first started using QE 6.0 not long ago I had trouble using<br>
> crystal_sg<br>
><br>
> Why?<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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> e61d2cfd/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 6<br>
> Date: Thu, 23 Feb 2017 21:45:36 +0100<br>
> From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
> Subject: Re: [Pw_forum] Symmetry recognition<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID:<br>
> <CAPMgbCtiYOpZxFHY0H+-xFJb2c=<wbr>a+5dM15xO0C_LB4LRH4+uqw@mail.<br>
> <a href="http://gmail.com" rel="noreferrer" target="_blank">gmail.com</a>><br>
> Content-Type: text/plain; charset=UTF-8<br>
><br>
> Of course there is a reason, but not necessarily a good one. If you<br>
> are "restarting from an incomplete calculation", I guess that the code<br>
> overwrites the input coordinates with the current ones. The symmetry<br>
> should be the same, but sometimes numerical noise breaks the symmetry.<br>
> It is impossible to say more without an example.<br>
><br>
> Paolo<br>
><br>
> On Thu, Feb 23, 2017 at 8:56 AM, Pascal Boulet<br>
> <<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>> wrote:<br>
> > Dear all,<br>
> ><br>
> > I am running a structural optimization with QE 6.0. The structure is<br>
> > orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not<br>
> > converge so I have to restart it. But as I restart it, the number of<br>
> > symmetry is now 4, there is a descent of symmetry. I shall say that I use<br>
> > the space_group option with COORDINATES crystal_sg. But the problem<br>
> remains<br>
> > if I put all the coordinates (unsurprisingly).<br>
> ><br>
> > Is there a reason for this, and can I avoid this?<br>
> ><br>
> > Thank you<br>
> > Best regards<br>
> > Pascal<br>
> ><br>
> > -<br>
> > Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE<br>
> > Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie<br>
> Niemen -<br>
> > 13013 Marseille<br>
> > T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50<br>
> > Site : <a href="http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire" rel="noreferrer" target="_blank">http://madirel.univ-amu.fr/<wbr>pages_web_BOULET_PASCAL/<wbr>annuaire</a> -<br>
> Email :<br>
> > <a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > ______________________________<wbr>_________________<br>
> > Pw_forum mailing list<br>
> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
><br>
><br>
><br>
> --<br>
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
> Phone +39-0432-558216, fax +39-0432-558222<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 7<br>
> Date: Fri, 24 Feb 2017 11:32:45 +0530<br>
> From: Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
> Subject: [Pw_forum] (no subject)<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Message-ID:<br>
> <CAPLukqnb5yf+k8-<wbr>EmkMwitWeiGZcx_<wbr>PrasB1MRigfGyRwBe9Sg@mail.<br>
> <a href="http://gmail.com" rel="noreferrer" target="_blank">gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hello everybody<br>
> I am getting wrong charge error as given below, in my output file:<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> * WARNING: integrated charge= 6.02151254, expected=<br>
> 6.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> Error in routine electrons (1): charge is<br>
> wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> stopping ...*<br>
><br>
> I have checked the FAQ section of QE website where the solution is given as<br>
> to use a gaussian smearing. I am using a gaussian smearing for my metallic<br>
> system, still the error.<br>
><br>
> I am copying my input file contents below:<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> * &CONTROL calculation = 'vc-relax' ,<br>
> restart_mode = 'from_scratch' , outdir = './tmp'<br>
> , pseudo_dir = '/home/sunetra/Desktop/In_qe/'<br>
> , prefix = 'In_vc-relax' , lkpoint_dir<br>
> = .true. , verbosity = 'high' ,<br>
> tstress = .true. , tprnfor = .true. ,<br>
> forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10<br>
> , / &SYSTEM ibrav = 0, nat =<br>
> 2, ntyp = 1, ecutwfc = 30<br>
> , nbnd = 10, occupations =<br>
> 'smearing' , degauss = 0.06 ,<br>
> smearing = 'gaussian' , input_dft = 'PBE'<br>
> , / &ELECTRONS electron_maxstep = 3000,<br>
> scf_must_converge = .true. , conv_thr = 1D-10<br>
> , mixing_beta = 0.7 , mixing_mode = 'plain'<br>
> , mixing_ndim = 8 , diagonalization = 'cg'<br>
> , diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS<br>
> Angstrom 4.953665310 0.000000000 0.000000000 2.476832660<br>
> 4.290000000 0.000000000 0.000000000 0.000000000 20.000000000<br>
> ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom<br>
> In 2.476832660 1.430000000 0.000000000 In<br>
> 4.953665310 2.860000000 0.000000000 K_POINTS automatic 31 31 1<br>
> 0 0 0 *<br>
> Kindly guide me in this matter. Thank you.<br>
> Regards,<br>
> Sunetra Das<br>
> -------------- next part --------------<br>
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> d49cd209/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 8<br>
> Date: Fri, 24 Feb 2017 11:41:07 +0530<br>
> From: Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
> Subject: [Pw_forum] Charge is wrong error<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Message-ID:<br>
> <CAPLukqm1kSk-<wbr>VFg7eMjJGPmHVeZfUwK=0qZW+<br>
> <a href="mailto:nRxuVF5SC%2B4YA@mail.gmail.com">nRxuVF5SC+4YA@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hello everybody<br>
> I am getting wrong charge error as given below, in my output file:<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> * WARNING: integrated charge= 6.02151254, expected=<br>
> 6.00000000 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> Error in routine electrons (1): charge is<br>
> wrong %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> stopping ...*<br>
><br>
> I have checked the FAQ section of QE website where the solution is given as<br>
> to use a gaussian smearing. I am using a gaussian smearing for my metallic<br>
> system, still the error.<br>
> I am using QE version 5.0.3. Also the error occurs after several<br>
> iterations.<br>
> I am copying my input file contents below:<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> * &CONTROL calculation = 'vc-relax' ,<br>
> restart_mode = 'from_scratch' , outdir = './tmp'<br>
> , pseudo_dir = '/home/sunetra/Desktop/In_qe/'<br>
> , prefix = 'In_vc-relax' , lkpoint_dir<br>
> = .true. , verbosity = 'high' ,<br>
> tstress = .true. , tprnfor = .true. ,<br>
> forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10<br>
> , / &SYSTEM ibrav = 0, nat =<br>
> 2, ntyp = 1, ecutwfc = 30<br>
> , nbnd = 10, occupations =<br>
> 'smearing' , degauss = 0.06 ,<br>
> smearing = 'gaussian' , input_dft = 'PBE'<br>
> , / &ELECTRONS electron_maxstep = 3000,<br>
> scf_must_converge = .true. , conv_thr = 1D-10<br>
> , mixing_beta = 0.7 , mixing_mode = 'plain'<br>
> , mixing_ndim = 8 , diagonalization = 'cg'<br>
> , diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS<br>
> Angstrom 4.953665310 0.000000000 0.000000000 2.476832660<br>
> 4.290000000 0.000000000 0.000000000 0.000000000 20.000000000<br>
> ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom<br>
> In 2.476832660 1.430000000 0.000000000 In<br>
> 4.953665310 2.860000000 0.000000000 K_POINTS automatic 31 31 1<br>
> 0 0 0 *<br>
> Kindly can anyone please guide me in this matter? Thank you.<br>
> Regards,<br>
> Sunetra Das<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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> db4ef4fd/attachment-0001.html<br>
><br>
> ------------------------------<br>
><br>
> Message: 9<br>
> Date: Fri, 24 Feb 2017 01:54:43 -0500<br>
> From: Jing Yang <<a href="mailto:yang15@sas.upenn.edu">yang15@sas.upenn.edu</a>><br>
> Subject: Re: [Pw_forum] Charge is wrong error<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID: <<a href="mailto:137AC56B-A1F5-4A32-88DE-44090A4A5D72@sas.upenn.edu">137AC56B-A1F5-4A32-88DE-<wbr>44090A4A5D72@sas.upenn.edu</a>><br>
> Content-Type: text/plain; charset="us-ascii"<br>
><br>
> In some cases, this indicates your pseudopotential is not good or initial<br>
> configuration is wrong ... Try use a different pseudopotential then.<br>
><br>
> Thanks,<br>
> Jing Yang<br>
><br>
> > On Feb 24, 2017, at 1:11 AM, Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
> wrote:<br>
> ><br>
> > Hello everybody<br>
> > I am getting wrong charge error as given below, in my output file:<br>
> ><br>
> > WARNING: integrated charge= 6.02151254, expected= 6.00000000<br>
> ><br>
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> > Error in routine electrons (1):<br>
> > charge is wrong<br>
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> %%%%%%%%%%%%%%%%%%<br>
> ><br>
> > stopping ...<br>
> ><br>
> > I have checked the FAQ section of QE website where the solution is given<br>
> as to use a gaussian smearing. I am using a gaussian smearing for my<br>
> metallic system, still the error.<br>
> > I am using QE version 5.0.3. Also the error occurs after several<br>
> iterations.<br>
> > I am copying my input file contents below:<br>
> ><br>
> > &CONTROL<br>
> > calculation = 'vc-relax' ,<br>
> > restart_mode = 'from_scratch' ,<br>
> > outdir = './tmp' ,<br>
> > pseudo_dir = '/home/sunetra/Desktop/In_qe/' ,<br>
> > prefix = 'In_vc-relax' ,<br>
> > lkpoint_dir = .true. ,<br>
> > verbosity = 'high' ,<br>
> > tstress = .true. ,<br>
> > tprnfor = .true. ,<br>
> > forc_conv_thr = 1.0D-2 ,<br>
> > etot_conv_thr = 10.0D-10 ,<br>
> ><br>
> > /<br>
> > &SYSTEM<br>
> > ibrav = 0,<br>
> > nat = 2,<br>
> > ntyp = 1,<br>
> > ecutwfc = 30 ,<br>
> > nbnd = 10,<br>
> > occupations = 'smearing' ,<br>
> > degauss = 0.06 ,<br>
> > smearing = 'gaussian' ,<br>
> > input_dft = 'PBE' ,<br>
> > /<br>
> > &ELECTRONS<br>
> > electron_maxstep = 3000,<br>
> > scf_must_converge = .true. ,<br>
> > conv_thr = 1D-10 ,<br>
> > mixing_beta = 0.7 ,<br>
> > mixing_mode = 'plain' ,<br>
> > mixing_ndim = 8 ,<br>
> > diagonalization = 'cg' ,<br>
> > diago_cg_maxiter = 3000 ,<br>
> > /<br>
> > &ions<br>
> > /<br>
> > &cell<br>
> > /<br>
> > CELL_PARAMETERS Angstrom<br>
> > 4.953665310 0.000000000 0.000000000<br>
> > 2.476832660 4.290000000 0.000000000<br>
> > 0.000000000 0.000000000 20.000000000<br>
> > ATOMIC_SPECIES<br>
> > In 114.81800 In.pbe-hgh.UPF<br>
> > ATOMIC_POSITIONS Angstrom<br>
> > In 2.476832660 1.430000000 0.000000000<br>
> > In 4.953665310 2.860000000 0.000000000<br>
> > K_POINTS automatic<br>
> > 31 31 1 0 0 0<br>
> ><br>
> > Kindly can anyone please guide me in this matter? Thank you.<br>
> > Regards,<br>
> > Sunetra Das<br>
> ><br>
> > ______________________________<wbr>_________________<br>
> > Pw_forum mailing list<br>
> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
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><br>
> ------------------------------<br>
><br>
> Message: 10<br>
> Date: Fri, 24 Feb 2017 10:09:00 +0100<br>
> From: alberto <<a href="mailto:voodoo.bender@gmail.com">voodoo.bender@gmail.com</a>><br>
> Subject: [Pw_forum] basis set module PROJWFC<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Message-ID:<br>
> <CAJKZiECH-kcJkiyC_<wbr>TNxKUTsdLknfKHCgS2P9Zssy+<br>
> <a href="mailto:7GoD7WOA@mail.gmail.com">7GoD7WOA@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi,<br>
> I have a question about the projections of band structure with *PROJWFC.<br>
> *what<br>
> basis set is used for the creation of the projections of the bands (e.g.,<br>
> double zeta, triple zeta, etc.)? In particular my model have got Sn and I.<br>
><br>
> Al<br>
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> ------------------------------<br>
><br>
> Message: 11<br>
> Date: Fri, 24 Feb 2017 10:36:03 +0100<br>
> From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
> Subject: Re: [Pw_forum] About output of PDOS calculations of CeO2<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Message-ID: <36291620.ELma9kdhud@amore2><br>
> Content-Type: text/plain; charset="ISO-8859-1"<br>
><br>
><br>
> Dear Phanikumar<br>
><br>
> PDOS is not affected by orbital occupation. Occupied orbitals in your plot<br>
> are those below the Fermi level of your system, which is printed in the pw.x<br>
> output.<br>
> HTH<br>
> Giuseppe<br>
><br>
> On Thursday, February 23, 2017 11:52:01 AM Phanikumar Pentyala wrote:<br>
> > Thank you Giuseppe Mattioli and Paolo Giannozzi<br>
> ><br>
> > The order of orbitals it calculates energy values already discussed by<br>
> > Paolo Giannozzi. But, in my system it contains *4f* have 7 orbitals in<br>
> it.<br>
> > but all will not fill during electron localizations (only first two<br>
> > orbitals). so my doubt was what is the use of remaining line of values in<br>
> > above attached document and which orbital values I have to choose in my<br>
> > graph?<br>
> ><br>
> > Please bare with my technical knowledge because I am not a background<br>
> from<br>
> > science<br>
> ><br>
> > Thank you once again<br>
> ><br>
> ><br>
> > Regards<br>
> > Phanikumar<br>
> ><br>
> ><br>
> > On Wed, Feb 22, 2017 at 7:14 PM, Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
> ><br>
> > wrote:<br>
> > > The order of Y_{lm}(\theta,\phi) is described here:<br>
> > > <a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/pp_" rel="noreferrer" target="_blank">http://www.quantum-espresso.<wbr>org/wp-content/uploads/Doc/pp_</a><br>
> > > user_guide/node8.html<br>
> > > For l=3 the sequence continues with: P_{3,0}, P_{3,1}cos(\phi),<br>
> > > P_{3,1}sin(\phi), P_{3,2}cos(2\phi), P_{3,2}sin(2\phi),<br>
> > > P_{3,3}cos(3\phi), P_{3,3}sin(3\phi)<br>
> > ><br>
> > > Paolo<br>
> > ><br>
> > > On Wed, Feb 22, 2017 at 2:16 PM, Giuseppe Mattioli<br>
> > ><br>
> > > <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>> wrote:<br>
> > > > Dear Phanikumar<br>
> > > > If I understand well your question, the pdos file attached to your<br>
> > ><br>
> > > previous message should contain 9 columns: the energy scale of PDOS,<br>
> the<br>
> > > total 4f<br>
> > ><br>
> > > > PDOS and the PDOS of the seven 4f orbitals (if you sum column 3-9 you<br>
> > ><br>
> > > obtain column 2). As opposed to the l=1 and l=2 cases, the symmetry<br>
> order of<br>
> > ><br>
> > > > orbitals in the l=3 case is not reported in the projwfc manual, but<br>
> > ><br>
> > > maybe there is someone more skilled than me that know the right<br>
> order...<br>
> > ><br>
> > > > HTH<br>
> > > > Giuseppe<br>
> > > ><br>
> > > > On Wednesday, February 22, 2017 05:18:40 PM Phanikumar Pentyala<br>
> wrote:<br>
> > > >> Thnk you Lorenzo Paulatto for quick reply<br>
> > > >><br>
> > > >> Yes I am doing DFT+U calculations. 4f will be in the valance bands<br>
> of Ce<br>
> > > >> atom. Because of redox property of *Ce*, electron localization take<br>
> > ><br>
> > > place.<br>
> > ><br>
> > > >> Here I am attaching my out put file of PDOS. Also I am using GGA<br>
> (PBE)<br>
> > > >> functional, NORM-CONSERVING potentials for my calculation.<br>
> > > >><br>
> > > >><br>
> > > >> On Wed, Feb 22, 2017 at 5:02 PM, Lorenzo Paulatto <<br>
> > > >><br>
> > > >> <a href="mailto:lorenzo.paulatto@impmc.upmc.fr">lorenzo.paulatto@impmc.upmc.fr</a><wbr>> wrote:<br>
> > > >> > On Wednesday, February 22, 2017 12:18:31 PM CET Phanikumar<br>
> Pentyala<br>
> > ><br>
> > > wrote:<br>
> > > >> > > My doubt was, cerium electronic structure have only single or<br>
> double<br>
> > > >> > > electron in *f* shell, so can I choose third or fourth line of<br>
> PDOS<br>
> > > >> ><br>
> > > >> > output<br>
> > > >> ><br>
> > > >> > > file or last line (first line belongs to LDOS)?<br>
> > > >> ><br>
> > > >> > Dear Phanikumar,<br>
> > > >> > the pseudopotential you are using for Cerium may or may not have<br>
> the f<br>
> > > >> > electron in valence.<br>
> > > >> ><br>
> > > >> > If the electron is in valence you will have a corresponding file<br>
> > ><br>
> > > after the<br>
> > ><br>
> > > >> > projwfc calculation. But your system will probably be metallica<br>
> and<br>
> > ><br>
> > > have<br>
> > ><br>
> > > >> > all<br>
> > > >> > sort of problems, unless you use DFT+U and know what you are<br>
> doing.<br>
> > > >> ><br>
> > > >> > If it is in the core, you won't be able to compute its pdos (which<br>
> > ><br>
> > > anyway,<br>
> > ><br>
> > > >> > is<br>
> > > >> > a delta function at the atomic state energy). Also your valence<br>
> bands<br>
> > ><br>
> > > will<br>
> > ><br>
> > > >> > miss some feature and probably be not completely correct.<br>
> > > >> > On the other hand, you will be able to get the calculation working<br>
> > ><br>
> > > without<br>
> > ><br>
> > > >> > too<br>
> > > >> > much fiddling.<br>
> > > >> ><br>
> > > >> ><br>
> > > >> > hth<br>
> > > >> ><br>
> > > >> > --<br>
> > > >> > Dr. Lorenzo Paulatto<br>
> > > >> > IdR @ IMPMC -- CNRS & Universit? Paris 6<br>
> > > >> > phone: +33 (0)1 442 79822 / skype: paulatz<br>
> > > >> > www: <a href="http://www-int.impmc.upmc.fr/~paulatto/" rel="noreferrer" target="_blank">http://www-int.impmc.upmc.fr/~<wbr>paulatto/</a><br>
> > > >> > mail: 23-24/423 Bo?te courrier 115, 4 place Jussieu 75252 Paris<br>
> > ><br>
> > > C?dex 05<br>
> > ><br>
> > > >> > ______________________________<wbr>_________________<br>
> > > >> > Pw_forum mailing list<br>
> > > >> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > > >> > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
> > > ><br>
> > > > ******************************<wbr>**************************<br>
> > > > - Article premier - Les hommes naissent et demeurent<br>
> > > > libres et ?gaux en droits. Les distinctions sociales<br>
> > > > ne peuvent ?tre fond?es que sur l'utilit? commune<br>
> > > > - Article 2 - Le but de toute association politique<br>
> > > > est la conservation des droits naturels et<br>
> > > > imprescriptibles de l'homme. Ces droits sont la libert?,<br>
> > > > la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
> > > > ******************************<wbr>**************************<br>
> > > ><br>
> > > > Giuseppe Mattioli<br>
> > > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
> > > > v. Salaria Km 29,300 - C.P. 10<br>
> > > > I 00015 - Monterotondo Stazione (RM), Italy<br>
> > > > Tel + 39 06 90672342 - Fax +39 06 90672316<br>
> > > > E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
> > > > <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
> > > > ResearcherID: F-6308-2012<br>
> > > ><br>
> > > > ______________________________<wbr>_________________<br>
> > > > Pw_forum mailing list<br>
> > > > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > > > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
> > ><br>
> > > --<br>
> > > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
> > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
> > > Phone +39-0432-558216, fax +39-0432-558222<br>
> > ><br>
> > > ______________________________<wbr>_________________<br>
> > > Pw_forum mailing list<br>
> > > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
><br>
> ******************************<wbr>**************************<br>
> - Article premier - Les hommes naissent et demeurent<br>
> libres et ?gaux en droits. Les distinctions sociales<br>
> ne peuvent ?tre fond?es que sur l'utilit? commune<br>
> - Article 2 - Le but de toute association politique<br>
> est la conservation des droits naturels et<br>
> imprescriptibles de l'homme. Ces droits sont la libert?,<br>
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
> ******************************<wbr>**************************<br>
><br>
> Giuseppe Mattioli<br>
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
> v. Salaria Km 29,300 - C.P. 10<br>
> I 00015 - Monterotondo Stazione (RM), Italy<br>
> Tel + 39 06 90672342 - Fax +39 06 90672316<br>
> E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
> <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
> ResearcherID: F-6308-2012<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 12<br>
> Date: Fri, 24 Feb 2017 10:50:41 +0100<br>
> From: Lorenzo Paulatto <<a href="mailto:lorenzo.paulatto@impmc.upmc.fr">lorenzo.paulatto@impmc.upmc.<wbr>fr</a>><br>
> Subject: Re: [Pw_forum] basis set module PROJWFC<br>
> To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
> Message-ID: <1966835.skiQF9jZZP@naquite><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> On Friday, February 24, 2017 10:09:00 AM CET alberto wrote:<br>
> > I have a question about the projections of band structure with *PROJWFC.<br>
> > *what basis set is used for the creation of the projections of the bands<br>
> > (e.g., double zeta, triple zeta, etc.)? In particular my model have got<br>
> Sn<br>
> > and I.<br>
><br>
> Dear Alberto,<br>
> projwfc.x projects on the atomic wavefunctions that are included in the<br>
> pesudopotential file. Check the header of the file to have more details.<br>
><br>
> kind regards<br>
><br>
> --<br>
> Dr. Lorenzo Paulatto<br>
> IdR @ IMPMC -- CNRS & Universit? Paris 6<br>
> phone: +33 (0)1 442 79822 / skype: paulatz<br>
> www: <a href="http://www-int.impmc.upmc.fr/~paulatto/" rel="noreferrer" target="_blank">http://www-int.impmc.upmc.fr/~<wbr>paulatto/</a><br>
> mail: 23-24/423 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05<br>
><br>
><br>
><br>
> ------------------------------<br>
><br>
> ______________________________<wbr>_________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
><br>
> End of Pw_forum Digest, Vol 115, Issue 24<br>
> ******************************<wbr>***********<br>
><br>
><br>
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<br>
Message: 2<br>
Date: Fri, 24 Feb 2017 23:24:31 +0900<br>
From: Minoru Otani <<a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.jp</a>><br>
Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and<br>
Otani/Sugino example<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:138FACE9-ECDC-4FD8-B88A-1869212621C1@aist.go.jp">138FACE9-ECDC-4FD8-B88A-<wbr>1869212621C1@aist.go.jp</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear Louis,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Best regards,<br>
Minoru<br>
<br>
------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>--------------<br>
Minoru Otani<br>
National Institute of Advanced Industrial Science and Technology<br>
Research Centre for Computational Design of Advanced Functional Materials<br>
email : <a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.jp</a> <mailto:<a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.<wbr>jp</a>><br>
------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>---------------<br>
<br>
> On Feb 23, 2017, at 21:42, Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>> wrote:<br>
><br>
> Hi there,<br>
><br>
> 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.<br>
><br>
> I have a few questions:<br>
><br>
> ** 1. ** In the QE example the following cell params and atomic positions are specified:<br>
><br>
> CELL_PARAMETERS bohr<br>
> 10.82227686 0.00000000 0.00000000<br>
> 0.00000000 10.82227686 0.00000000<br>
> 0.00000000 0.00000000 22.67672253<br>
> ATOMIC_POSITIONS bohr<br>
> Al 0.00000000 0.00000000 0.00000000<br>
> Al 5.41113843 0.00000000 0.00000000<br>
> Al 0.00000000 5.41113843 0.00000000<br>
> Al 5.41113843 5.41113843 0.00000000<br>
><br>
> 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?<br>
><br>
> 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?<br>
><br>
> ** 2. ** I have reproduced the 'surface unit cell' from Otani/Sugino's paper using VESTA.<br>
><br>
> 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.<br>
><br>
> 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?<br>
><br>
> 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?<br>
><br>
> Thank you for your time and sorry for the very long email,<br>
> Kindest regards,<br>
> Louis<br>
><br>
> ______________________________<wbr>_________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a> <mailto:<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a> <<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a>><br>
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Message: 3<br>
Date: Fri, 24 Feb 2017 15:44:25 +0100<br>
From: Pascal Boulet <<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>><br>
Subject: Re: [Pw_forum] Symmetry recognition<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:89481035-37BD-45FD-9665-1F4E49FBDD9F@univ-amu.fr">89481035-37BD-45FD-9665-<wbr>1F4E49FBDD9F@univ-amu.fr</a>><br>
Content-Type: text/plain; charset=windows-1252<br>
<br>
Dear all,<br>
<br>
Thank you for your answers. I am trying to reproduce it with a smaller system? I indeed restart from an incomplete calculation.<br>
<br>
Pascal<br>
<br>
<br>
<br>
Le 23 f?vr. 2017 ? 21:45, Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>> a ?crit :<br>
<br>
> Of course there is a reason, but not necessarily a good one. If you<br>
> are "restarting from an incomplete calculation", I guess that the code<br>
> overwrites the input coordinates with the current ones. The symmetry<br>
> should be the same, but sometimes numerical noise breaks the symmetry.<br>
> It is impossible to say more without an example.<br>
><br>
> Paolo<br>
><br>
> On Thu, Feb 23, 2017 at 8:56 AM, Pascal Boulet<br>
> <<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>> wrote:<br>
>> Dear all,<br>
>><br>
>> I am running a structural optimization with QE 6.0. The structure is<br>
>> orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not<br>
>> converge so I have to restart it. But as I restart it, the number of<br>
>> symmetry is now 4, there is a descent of symmetry. I shall say that I use<br>
>> the space_group option with COORDINATES crystal_sg. But the problem remains<br>
>> if I put all the coordinates (unsurprisingly).<br>
>><br>
>> Is there a reason for this, and can I avoid this?<br>
>><br>
>> Thank you<br>
>> Best regards<br>
>> Pascal<br>
>><br>
>> -<br>
>> Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE<br>
>> Aix-Marseille Universit? - ST JEROME - Avenue Escadrille Normandie Niemen -<br>
>> 13013 Marseille<br>
>> T?l: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50<br>
>> Site : <a href="http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire" rel="noreferrer" target="_blank">http://madirel.univ-amu.fr/<wbr>pages_web_BOULET_PASCAL/<wbr>annuaire</a> - Email :<br>
>> <a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> ______________________________<wbr>_________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
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><br>
><br>
><br>
> --<br>
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
> Phone +39-0432-558216, fax +39-0432-558222<br>
><br>
> ______________________________<wbr>_________________<br>
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<br>
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------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 24 Feb 2017 15:14:30 +0000<br>
From: Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and<br>
Otani/Sugino example<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:DB5PR0301MB194286ED6BC8DB80EFB586B19E520@DB5PR0301MB1942.eurprd03.prod.outlook.com">DB5PR0301MB194286ED6BC8DB80EF<wbr>B586B19E520@DB5PR0301MB1942.<wbr>eurprd03.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Minoru,<br>
<br>
<br>
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!<br>
<br>
<br>
Kindest regards,<br>
<br>
Louis<br>
<br>
______________________________<wbr>__<br>
From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on behalf of Minoru Otani <<a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.jp</a>><br>
Sent: 24 February 2017 14:24:31<br>
To: PWSCF Forum<br>
Subject: Re: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino example<br>
<br>
Dear Louis,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Best regards,<br>
Minoru<br>
<br>
------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>--------------<br>
Minoru Otani<br>
National Institute of Advanced Industrial Science and Technology<br>
Research Centre for Computational Design of Advanced Functional Materials<br>
email : <a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.jp</a><<wbr>mailto:<a href="mailto:minoru.otani@aist.go.jp">minoru.otani@aist.go.jp</a><wbr>><br>
------------------------------<wbr>------------------------------<wbr>------------------------------<wbr>---------------<br>
<br>
On Feb 23, 2017, at 21:42, Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a><mailto:<a href="mailto:ellf@leeds.ac.uk">ellf@<wbr>leeds.ac.uk</a>>> wrote:<br>
<br>
<br>
Hi there,<br>
<br>
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.<br>
<br>
I have a few questions:<br>
<br>
** 1. ** In the QE example the following cell params and atomic positions are specified:<br>
<br>
CELL_PARAMETERS bohr<br>
10.82227686 0.00000000 0.00000000<br>
0.00000000 10.82227686 0.00000000<br>
0.00000000 0.00000000 22.67672253<br>
ATOMIC_POSITIONS bohr<br>
Al 0.00000000 0.00000000 0.00000000<br>
Al 5.41113843 0.00000000 0.00000000<br>
Al 0.00000000 5.41113843 0.00000000<br>
Al 5.41113843 5.41113843 0.00000000<br>
<br>
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?<br>
<br>
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?<br>
<br>
** 2. ** I have reproduced the 'surface unit cell' from Otani/Sugino's paper using VESTA.<br>
<br>
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.<br>
<br>
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?<br>
<br>
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?<br>
<br>
Thank you for your time and sorry for the very long email,<br>
Kindest regards,<br>
Louis<br>
<br>
<br>
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Message: 5<br>
Date: Fri, 24 Feb 2017 18:30:47 +0300<br>
From: Semen Yesylevskyy <<a href="mailto:yesint@mail.ru">yesint@mail.ru</a>><br>
Subject: [Pw_forum] All Lowdin charges are zero<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <<a href="mailto:1487950247.124921620@f401.i.mail.ru">1487950247.124921620@f401.i.<wbr>mail.ru</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear All,<br>
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:<br>
<br>
Lowdin Charges:<br>
??? ?<br>
???? Atom #?? 1: total charge =?? 0.0000, s =? 0.0000,<br>
???? Atom #?? 1: total charge =?? 0.0000, p =? 0.0000, pz=? 0.0000, px=? 0.0000, py=? 0.0000,<br>
???? Atom #?? 2: total charge =?? 0.0001, s =? 0.0000,<br>
???? Atom #?? 2: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=? 0.0000, py=? 0.0000,<br>
???? Atom #?? 3: total charge =?? 0.0001, s =? 0.0000,<br>
???? Atom #?? 3: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=? 0.0000, py=? 0.0000,<br>
???? Atom #?? 4: total charge =?? 0.0000, s =? 0.0000,<br>
???? Atom #?? 4: total charge =?? 0.0000, p =? 0.0000, pz=? 0.0000, px=? 0.0000, py=? 0.0000,<br>
???? Atom #?? 5: total charge =?? 0.0001, s =? 0.0000,<br>
???? Atom #?? 5: total charge =?? 0.0001, p =? 0.0001, pz=? 0.0000, px=? 0.0000, py=? 0.0000,<br>
???? Atom #?? 6: total charge =?? 0.0001, s =? 0.0000,<br>
....<br>
<br>
Could you please give me some advice of what I'm doing wrong?<br>
<br>
------------------------------<wbr>--<br>
The projwcf input:<br>
<br>
?&PROJWFC<br>
????????????????????? prefix = './3cell-cb_scf' ,<br>
????????????????????? outdir = '.' ,<br>
????????????????????? ngauss = 0.1 ,<br>
????????????????????? DeltaE = 0.01 ,<br>
?/<br>
<br>
------------------------------<wbr>--<br>
The scf input:<br>
<br>
?&CONTROL<br>
???????????????? calculation = 'scf' ,<br>
??????????????? restart_mode = 'from_scratch' ,<br>
????????????????????? outdir = '.' ,<br>
????????????????????? wfcdir = './tmp' ,<br>
????????????????? pseudo_dir = '.' ,<br>
????????????????????? prefix = '3cell-cb_scf' ,<br>
?????????????????????? nstep = 1000 ,<br>
???????????????????? tstress = .false. ,<br>
?/<br>
?&SYSTEM<br>
?????????????????????? ibrav = 4 ,<br>
?????????????????????????? A = 9.495 ,<br>
?????????????????????????? B = 9.495 ,<br>
?????????????????????????? C = 100.0 ,<br>
?????????????????????? cosAB = 0.5 ,<br>
?????????????????????? cosAC = 0 ,<br>
?????????????????????? cosBC = 0 ,<br>
???????????????????????? nat = 39,<br>
??????????????????????? ntyp = 5,<br>
???????????????????? ecutwfc = 35 ,<br>
???????????????????? ecutrho = 140 ,<br>
?????????????????????? nosym = .true. ,<br>
????????????????? tot_charge = 0.000000 ,<br>
?/<br>
?&ELECTRONS<br>
??????????? electron_maxstep = 200 ,<br>
??????????? scf_must_converge = .false. ,<br>
??????????? diagonalization='cg' ,<br>
?/<br>
?&IONS<br>
??????????????? ion_dynamics = 'bfgs' ,<br>
?/<br>
ATOMIC_SPECIES<br>
?? Mo?? 95.96?? Mo_ONCV_PBE-1.0.upf<br>
??? S?? 32.06?? S_pbe_v1.2.uspp.F.UPF<br>
??? C?? 12.011? C_pbe_v1.2.uspp.F.UPF<br>
??? H?? 1.008?? H.pbe-rrkjus_psl.0.1.UPF<br>
?? Cl?? 35.45?? cl_pbe_v1.4.uspp.F.UPF<br>
ATOMIC_POSITIONS angstrom<br>
Mo?????? 1.392123361?? 1.675146760?? 5.927158394<br>
S??????? 1.409356288?? 3.492127081?? 4.353797199<br>
S??????? 1.409009361?? 3.492914431?? 7.500696022<br>
Mo?????? 2.974783806?? 4.416004278?? 5.927352435<br>
S??????? 2.991861295?? 6.232688291?? 4.353114990<br>
S??????? 2.991733615?? 6.233889787?? 7.500216780<br>
Mo?????? 4.557309411?? 7.156655993?? 5.926482117<br>
S??????? 4.574550104?? 8.974187415?? 4.353268832<br>
S??????? 4.573865790?? 8.974308816?? 7.499997172<br>
Mo?????? 4.556900653?? 1.675497042?? 5.926861427<br>
S??????? 4.573955171?? 3.492114510?? 4.352949498<br>
S??????? 4.574377417?? 3.492858021?? 7.500504130<br>
Mo?????? 6.139333906?? 4.416035304?? 5.926363713<br>
S??????? 6.156932316?? 6.232998289?? 4.352535948<br>
S??????? 6.156651090?? 6.233324282?? 7.500124138<br>
Mo?????? 7.721896396?? 7.156797182?? 5.926687354<br>
S??????? 7.739160210?? 8.974228888?? 4.353457824<br>
S??????? 7.739048493?? 8.974459743?? 7.500654977<br>
Mo?????? 7.722031044?? 1.675217921?? 5.926454615<br>
S??????? 7.739331052?? 3.492171149?? 4.352920557<br>
S??????? 7.738377057?? 3.492639347?? 7.499947690<br>
Mo?????? 9.304280720?? 4.416123626?? 5.927097215<br>
S??????? 9.321652087?? 6.232837357?? 4.353059451<br>
S??????? 9.321594176?? 6.234116854?? 7.500174405<br>
Mo????? 10.887047440?? 7.156845127?? 5.926347019<br>
S?????? 10.903965611?? 8.974283787?? 4.353226240<br>
S?????? 10.903829602?? 8.974680010?? 7.500128022<br>
C??????? 5.700416780?? 4.960942076? 11.705590151<br>
C??????? 5.786661978?? 6.354516349? 11.705273773<br>
C??????? 7.046391983?? 6.956535202? 11.705217371<br>
C??????? 8.203237318?? 6.173116561? 11.705190411<br>
C??????? 8.099168585?? 4.780492709? 11.705023203<br>
C??????? 6.846678887?? 4.164104064? 11.704869934<br>
Cl?????? 4.129012811?? 4.204270654? 11.705957792<br>
H??????? 4.877613854?? 6.955359406? 11.704377918<br>
H??????? 7.118320846?? 8.046628444? 11.704165169<br>
H??????? 9.184749419?? 6.647034640? 11.704328004<br>
H??????? 8.998646725?? 4.161998637? 11.704137157<br>
H??????? 6.757143341?? 3.077849963? 11.704290956<br>
K_POINTS automatic<br>
? 1 1 1?? 1 1 1<br>
<br>
<br>
<br>
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Message: 6<br>
Date: Fri, 24 Feb 2017 16:44:35 +0100<br>
From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
Subject: Re: [Pw_forum] All Lowdin charges are zero<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <8934804.clCi8xVGCZ@amore2><br>
Content-Type: text/plain; charset="ISO-8859-1"<br>
<br>
<br>
<br>
Dear Colleague (please sign always the posts with name and affiliation)<br>
<br>
ONCV PPs do not contain pseudowavefunctions, if you do not say to the Hamann's code to include them.<br>
Look for this old thread in the QE forum<br>
<br>
[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc<br>
<br>
That should contain all you need to rebuild a PP with wfcs and to obtain Lowdin charges with projwfc.x<br>
<br>
HTH<br>
Giuseppe<br>
<br>
<br>
On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:<br>
> Dear All,<br>
> 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<br>
> 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<br>
> what I can expect:<br>
><br>
> Lowdin Charges:<br>
><br>
> Atom # 1: total charge = 0.0000, s = 0.0000,<br>
> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> Atom # 2: total charge = 0.0001, s = 0.0000,<br>
> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> Atom # 3: total charge = 0.0001, s = 0.0000,<br>
> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> Atom # 4: total charge = 0.0000, s = 0.0000,<br>
> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> Atom # 5: total charge = 0.0001, s = 0.0000,<br>
> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> Atom # 6: total charge = 0.0001, s = 0.0000,<br>
> ....<br>
><br>
> Could you please give me some advice of what I'm doing wrong?<br>
><br>
> ------------------------------<wbr>--<br>
> The projwcf input:<br>
><br>
> &PROJWFC<br>
> prefix = './3cell-cb_scf' ,<br>
> outdir = '.' ,<br>
> ngauss = 0.1 ,<br>
> DeltaE = 0.01 ,<br>
> /<br>
><br>
> ------------------------------<wbr>--<br>
> The scf input:<br>
><br>
> &CONTROL<br>
> calculation = 'scf' ,<br>
> restart_mode = 'from_scratch' ,<br>
> outdir = '.' ,<br>
> wfcdir = './tmp' ,<br>
> pseudo_dir = '.' ,<br>
> prefix = '3cell-cb_scf' ,<br>
> nstep = 1000 ,<br>
> tstress = .false. ,<br>
> /<br>
> &SYSTEM<br>
> ibrav = 4 ,<br>
> A = 9.495 ,<br>
> B = 9.495 ,<br>
> C = 100.0 ,<br>
> cosAB = 0.5 ,<br>
> cosAC = 0 ,<br>
> cosBC = 0 ,<br>
> nat = 39,<br>
> ntyp = 5,<br>
> ecutwfc = 35 ,<br>
> ecutrho = 140 ,<br>
> nosym = .true. ,<br>
> tot_charge = 0.000000 ,<br>
> /<br>
> &ELECTRONS<br>
> electron_maxstep = 200 ,<br>
> scf_must_converge = .false. ,<br>
> diagonalization='cg' ,<br>
> /<br>
> &IONS<br>
> ion_dynamics = 'bfgs' ,<br>
> /<br>
> ATOMIC_SPECIES<br>
> Mo 95.96 Mo_ONCV_PBE-1.0.upf<br>
> S 32.06 S_pbe_v1.2.uspp.F.UPF<br>
> C 12.011 C_pbe_v1.2.uspp.F.UPF<br>
> H 1.008 H.pbe-rrkjus_psl.0.1.UPF<br>
> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF<br>
> ATOMIC_POSITIONS angstrom<br>
> Mo 1.392123361 1.675146760 5.927158394<br>
> S 1.409356288 3.492127081 4.353797199<br>
> S 1.409009361 3.492914431 7.500696022<br>
> Mo 2.974783806 4.416004278 5.927352435<br>
> S 2.991861295 6.232688291 4.353114990<br>
> S 2.991733615 6.233889787 7.500216780<br>
> Mo 4.557309411 7.156655993 5.926482117<br>
> S 4.574550104 8.974187415 4.353268832<br>
> S 4.573865790 8.974308816 7.499997172<br>
> Mo 4.556900653 1.675497042 5.926861427<br>
> S 4.573955171 3.492114510 4.352949498<br>
> S 4.574377417 3.492858021 7.500504130<br>
> Mo 6.139333906 4.416035304 5.926363713<br>
> S 6.156932316 6.232998289 4.352535948<br>
> S 6.156651090 6.233324282 7.500124138<br>
> Mo 7.721896396 7.156797182 5.926687354<br>
> S 7.739160210 8.974228888 4.353457824<br>
> S 7.739048493 8.974459743 7.500654977<br>
> Mo 7.722031044 1.675217921 5.926454615<br>
> S 7.739331052 3.492171149 4.352920557<br>
> S 7.738377057 3.492639347 7.499947690<br>
> Mo 9.304280720 4.416123626 5.927097215<br>
> S 9.321652087 6.232837357 4.353059451<br>
> S 9.321594176 6.234116854 7.500174405<br>
> Mo 10.887047440 7.156845127 5.926347019<br>
> S 10.903965611 8.974283787 4.353226240<br>
> S 10.903829602 8.974680010 7.500128022<br>
> C 5.700416780 4.960942076 11.705590151<br>
> C 5.786661978 6.354516349 11.705273773<br>
> C 7.046391983 6.956535202 11.705217371<br>
> C 8.203237318 6.173116561 11.705190411<br>
> C 8.099168585 4.780492709 11.705023203<br>
> C 6.846678887 4.164104064 11.704869934<br>
> Cl 4.129012811 4.204270654 11.705957792<br>
> H 4.877613854 6.955359406 11.704377918<br>
> H 7.118320846 8.046628444 11.704165169<br>
> H 9.184749419 6.647034640 11.704328004<br>
> H 8.998646725 4.161998637 11.704137157<br>
> H 6.757143341 3.077849963 11.704290956<br>
> K_POINTS automatic<br>
> 1 1 1 1 1 1<br>
<br>
******************************<wbr>**************************<br>
- Article premier - Les hommes naissent et demeurent<br>
libres et ?gaux en droits. Les distinctions sociales<br>
ne peuvent ?tre fond?es que sur l'utilit? commune<br>
- Article 2 - Le but de toute association politique<br>
est la conservation des droits naturels et<br>
imprescriptibles de l'homme. Ces droits sont la libert?,<br>
la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
******************************<wbr>**************************<br>
<br>
Giuseppe Mattioli<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
v. Salaria Km 29,300 - C.P. 10<br>
I 00015 - Monterotondo Stazione (RM), Italy<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
<a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
ResearcherID: F-6308-2012<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Fri, 24 Feb 2017 18:58:34 +0300<br>
From: Semen Yesylevskyy <<a href="mailto:yesint@mail.ru">yesint@mail.ru</a>><br>
Subject: Re: [Pw_forum] All Lowdin charges are zero<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:1487951914.308180464@f404.i.mail.ru">1487951914.308180464@f404.i.<wbr>mail.ru</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Giuseppe,<br>
Thank you for quick reply, but I hardly understand the terms and local moonspeak because I'm using Quantum Espresso for few days only.<br>
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.<br>
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:<br>
1) do optimization with pw.x<br>
2) do scf with pw.x<br>
3) run projwfc.x<br>
<br>
That is what I did without success...<br>
<br>
Sincerely,<br>
Dr. Semen Yesylevskyy<br>
<br>
Department of Physics of Biological Systems<br>
Institute of Physics of NAS of Ukraine<br>
<br>
<br>
>???????, 24 ??????? 2017, 17:44 +02:00 ?? Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><wbr>:<br>
><br>
><br>
><br>
>Dear Colleague (please sign always the posts with name and affiliation)<br>
><br>
>ONCV PPs do not contain pseudowavefunctions, if you do not say to the Hamann's code to include them.<br>
>Look for this old thread in the QE forum<br>
><br>
>[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc<br>
><br>
>That should contain all you need to rebuild a PP with wfcs and to obtain Lowdin charges with projwfc.x<br>
><br>
>HTH<br>
>Giuseppe<br>
><br>
><br>
>On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:<br>
>> Dear All,<br>
>> 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<br>
>> 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<br>
>> what I can expect:<br>
>><br>
>> Lowdin Charges:<br>
>><br>
>> Atom # 1: total charge = 0.0000, s = 0.0000,<br>
>> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> Atom # 2: total charge = 0.0001, s = 0.0000,<br>
>> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> Atom # 3: total charge = 0.0001, s = 0.0000,<br>
>> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> Atom # 4: total charge = 0.0000, s = 0.0000,<br>
>> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> Atom # 5: total charge = 0.0001, s = 0.0000,<br>
>> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> Atom # 6: total charge = 0.0001, s = 0.0000,<br>
>> ....<br>
>><br>
>> Could you please give me some advice of what I'm doing wrong?<br>
>><br>
>> ------------------------------<wbr>--<br>
>> The projwcf input:<br>
>><br>
>> &PROJWFC<br>
>> prefix = './3cell-cb_scf' ,<br>
>> outdir = '.' ,<br>
>> ngauss = 0.1 ,<br>
>> DeltaE = 0.01 ,<br>
>> /<br>
>><br>
>> ------------------------------<wbr>--<br>
>> The scf input:<br>
>><br>
>> &CONTROL<br>
>> calculation = 'scf' ,<br>
>> restart_mode = 'from_scratch' ,<br>
>> outdir = '.' ,<br>
>> wfcdir = './tmp' ,<br>
>> pseudo_dir = '.' ,<br>
>> prefix = '3cell-cb_scf' ,<br>
>> nstep = 1000 ,<br>
>> tstress = .false. ,<br>
>> /<br>
>> &SYSTEM<br>
>> ibrav = 4 ,<br>
>> A = 9.495 ,<br>
>> B = 9.495 ,<br>
>> C = 100.0 ,<br>
>> cosAB = 0.5 ,<br>
>> cosAC = 0 ,<br>
>> cosBC = 0 ,<br>
>> nat = 39,<br>
>> ntyp = 5,<br>
>> ecutwfc = 35 ,<br>
>> ecutrho = 140 ,<br>
>> nosym = .true. ,<br>
>> tot_charge = 0.000000 ,<br>
>> /<br>
>> &ELECTRONS<br>
>> electron_maxstep = 200 ,<br>
>> scf_must_converge = .false. ,<br>
>> diagonalization='cg' ,<br>
>> /<br>
>> &IONS<br>
>> ion_dynamics = 'bfgs' ,<br>
>> /<br>
>> ATOMIC_SPECIES<br>
>> Mo 95.96 Mo_ONCV_PBE-1.0.upf<br>
>> S 32.06 S_pbe_v1.2.uspp.F.UPF<br>
>> C 12.011 C_pbe_v1.2.uspp.F.UPF<br>
>> H 1.008 H.pbe-rrkjus_psl.0.1.UPF<br>
>> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF<br>
>> ATOMIC_POSITIONS angstrom<br>
>> Mo 1.392123361 1.675146760 5.927158394<br>
>> S 1.409356288 3.492127081 4.353797199<br>
>> S 1.409009361 3.492914431 7.500696022<br>
>> Mo 2.974783806 4.416004278 5.927352435<br>
>> S 2.991861295 6.232688291 4.353114990<br>
>> S 2.991733615 6.233889787 7.500216780<br>
>> Mo 4.557309411 7.156655993 5.926482117<br>
>> S 4.574550104 8.974187415 4.353268832<br>
>> S 4.573865790 8.974308816 7.499997172<br>
>> Mo 4.556900653 1.675497042 5.926861427<br>
>> S 4.573955171 3.492114510 4.352949498<br>
>> S 4.574377417 3.492858021 7.500504130<br>
>> Mo 6.139333906 4.416035304 5.926363713<br>
>> S 6.156932316 6.232998289 4.352535948<br>
>> S 6.156651090 6.233324282 7.500124138<br>
>> Mo 7.721896396 7.156797182 5.926687354<br>
>> S 7.739160210 8.974228888 4.353457824<br>
>> S 7.739048493 8.974459743 7.500654977<br>
>> Mo 7.722031044 1.675217921 5.926454615<br>
>> S 7.739331052 3.492171149 4.352920557<br>
>> S 7.738377057 3.492639347 7.499947690<br>
>> Mo 9.304280720 4.416123626 5.927097215<br>
>> S 9.321652087 6.232837357 4.353059451<br>
>> S 9.321594176 6.234116854 7.500174405<br>
>> Mo 10.887047440 7.156845127 5.926347019<br>
>> S 10.903965611 8.974283787 4.353226240<br>
>> S 10.903829602 8.974680010 7.500128022<br>
>> C 5.700416780 4.960942076 11.705590151<br>
>> C 5.786661978 6.354516349 11.705273773<br>
>> C 7.046391983 6.956535202 11.705217371<br>
>> C 8.203237318 6.173116561 11.705190411<br>
>> C 8.099168585 4.780492709 11.705023203<br>
>> C 6.846678887 4.164104064 11.704869934<br>
>> Cl 4.129012811 4.204270654 11.705957792<br>
>> H 4.877613854 6.955359406 11.704377918<br>
>> H 7.118320846 8.046628444 11.704165169<br>
>> H 9.184749419 6.647034640 11.704328004<br>
>> H 8.998646725 4.161998637 11.704137157<br>
>> H 6.757143341 3.077849963 11.704290956<br>
>> K_POINTS automatic<br>
>> 1 1 1 1 1 1<br>
><br>
>*****************************<wbr>***************************<br>
>- Article premier - Les hommes naissent et demeurent<br>
>libres et ?gaux en droits. Les distinctions sociales<br>
>ne peuvent ?tre fond?es que sur l'utilit? commune<br>
>- Article 2 - Le but de toute association politique<br>
>est la conservation des droits naturels et<br>
>imprescriptibles de l'homme. Ces droits sont la libert?,<br>
>la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
>*****************************<wbr>***************************<br>
><br>
>???Giuseppe Mattioli<br>
>???CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
>???v. Salaria Km 29,300 - C.P. 10<br>
>???I 00015 - Monterotondo Stazione (RM), Italy<br>
>???Tel + 39 06 90672342 - Fax +39 06 90672316<br>
>???E-mail: < <a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a> ><br>
>??? <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
>???ResearcherID: F-6308-2012<br>
><br>
>_____________________________<wbr>__________________<br>
>Pw_forum mailing list<br>
><a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
><a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
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<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Fri, 24 Feb 2017 17:40:55 +0100<br>
From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
Subject: Re: [Pw_forum] All Lowdin charges are zero<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <5515524.XkLPboe93X@amore2><br>
Content-Type: text/plain; charset="ISO-8859-1"<br>
<br>
<br>
Dear Semen<br>
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<br>
your-path-to Espresso-6.0/atomic/Doc/<wbr>pseudo-gen.pdf<br>
and some of the references contained therein.<br>
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<br>
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<br>
regarding the generation and usage of several kinds of pseudopotential.<br>
<br>
In your case, the optimized norm-conserving Vanderbilt's pseudopotentials (ONCV PPs) downloaded from this database<br>
<a href="http://www.quantum-simulation.org/potentials/sg15_oncv/" rel="noreferrer" target="_blank">http://www.quantum-simulation.<wbr>org/potentials/sg15_oncv/</a><br>
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<br>
orbitals and the Lowdin partition of valence charge.<br>
<br>
If you want to use such PPs you should<br>
<br>
a) download and install the Hamann's code<br>
<br>
b) re-generate the same PPs by yourself with the input you find in the header at the beginning of the PP file<br>
<br>
And this was explained by Lorenzo Paulatto in the old thread mentioned in my previous mail.<br>
<br>
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<br>
to try to find whether there is anybody who can do this work for you...:-)<br>
HTH<br>
Giuseppe<br>
<br>
On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote:<br>
> Dear Giuseppe,<br>
> Thank you for quick reply, but I hardly understand the terms and local moonspeak because I'm using Quantum Espresso for few days only.<br>
> 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<br>
> 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<br>
> extensively and the only thing which I've found is the following: 1) do optimization with pw.x<br>
> 2) do scf with pw.x<br>
> 3) run projwfc.x<br>
><br>
> That is what I did without success...<br>
><br>
> Sincerely,<br>
> Dr. Semen Yesylevskyy<br>
><br>
> Department of Physics of Biological Systems<br>
> Institute of Physics of NAS of Ukraine<br>
><br>
> >??????????????, 24 ?????????????? 2017, 17:44 +02:00 ???? Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><wbr>:<br>
> ><br>
> ><br>
> ><br>
> >Dear Colleague (please sign always the posts with name and affiliation)<br>
> ><br>
> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the Hamann's code to include them.<br>
> >Look for this old thread in the QE forum<br>
> ><br>
> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc<br>
> ><br>
> >That should contain all you need to rebuild a PP with wfcs and to obtain Lowdin charges with projwfc.x<br>
> ><br>
> >HTH<br>
> >Giuseppe<br>
> ><br>
> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:<br>
> >> Dear All,<br>
> >> 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<br>
> >> 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<br>
> >> not<br>
> >> what I can expect:<br>
> >><br>
> >> Lowdin Charges:<br>
> >> Atom # 1: total charge = 0.0000, s = 0.0000,<br>
> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> >> Atom # 2: total charge = 0.0001, s = 0.0000,<br>
> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> >> Atom # 3: total charge = 0.0001, s = 0.0000,<br>
> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> >> Atom # 4: total charge = 0.0000, s = 0.0000,<br>
> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> >> Atom # 5: total charge = 0.0001, s = 0.0000,<br>
> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
> >> Atom # 6: total charge = 0.0001, s = 0.0000,<br>
> >><br>
> >> ....<br>
> >><br>
> >> Could you please give me some advice of what I'm doing wrong?<br>
> >><br>
> >> ------------------------------<wbr>--<br>
> >><br>
> >> The projwcf input:<br>
> >> &PROJWFC<br>
> >><br>
> >> prefix = './3cell-cb_scf' ,<br>
> >> outdir = '.' ,<br>
> >> ngauss = 0.1 ,<br>
> >> DeltaE = 0.01 ,<br>
> >><br>
> >> /<br>
> >><br>
> >> ------------------------------<wbr>--<br>
> >><br>
> >> The scf input:<br>
> >> &CONTROL<br>
> >><br>
> >> calculation = 'scf' ,<br>
> >><br>
> >> restart_mode = 'from_scratch' ,<br>
> >><br>
> >> outdir = '.' ,<br>
> >> wfcdir = './tmp' ,<br>
> >><br>
> >> pseudo_dir = '.' ,<br>
> >><br>
> >> prefix = '3cell-cb_scf' ,<br>
> >><br>
> >> nstep = 1000 ,<br>
> >><br>
> >> tstress = .false. ,<br>
> >><br>
> >> /<br>
> >> &SYSTEM<br>
> >><br>
> >> ibrav = 4 ,<br>
> >><br>
> >> A = 9.495 ,<br>
> >> B = 9.495 ,<br>
> >> C = 100.0 ,<br>
> >><br>
> >> cosAB = 0.5 ,<br>
> >> cosAC = 0 ,<br>
> >> cosBC = 0 ,<br>
> >><br>
> >> nat = 39,<br>
> >><br>
> >> ntyp = 5,<br>
> >><br>
> >> ecutwfc = 35 ,<br>
> >> ecutrho = 140 ,<br>
> >><br>
> >> nosym = .true. ,<br>
> >><br>
> >> tot_charge = 0.000000 ,<br>
> >><br>
> >> /<br>
> >> &ELECTRONS<br>
> >><br>
> >> electron_maxstep = 200 ,<br>
> >> scf_must_converge = .false. ,<br>
> >> diagonalization='cg' ,<br>
> >><br>
> >> /<br>
> >> &IONS<br>
> >><br>
> >> ion_dynamics = 'bfgs' ,<br>
> >><br>
> >> /<br>
> >><br>
> >> ATOMIC_SPECIES<br>
> >><br>
> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf<br>
> >><br>
> >> S 32.06 S_pbe_v1.2.uspp.F.UPF<br>
> >> C 12.011 C_pbe_v1.2.uspp.F.UPF<br>
> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF<br>
> >><br>
> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF<br>
> >><br>
> >> ATOMIC_POSITIONS angstrom<br>
> >> Mo 1.392123361 1.675146760 5.927158394<br>
> >> S 1.409356288 3.492127081 4.353797199<br>
> >> S 1.409009361 3.492914431 7.500696022<br>
> >> Mo 2.974783806 4.416004278 5.927352435<br>
> >> S 2.991861295 6.232688291 4.353114990<br>
> >> S 2.991733615 6.233889787 7.500216780<br>
> >> Mo 4.557309411 7.156655993 5.926482117<br>
> >> S 4.574550104 8.974187415 4.353268832<br>
> >> S 4.573865790 8.974308816 7.499997172<br>
> >> Mo 4.556900653 1.675497042 5.926861427<br>
> >> S 4.573955171 3.492114510 4.352949498<br>
> >> S 4.574377417 3.492858021 7.500504130<br>
> >> Mo 6.139333906 4.416035304 5.926363713<br>
> >> S 6.156932316 6.232998289 4.352535948<br>
> >> S 6.156651090 6.233324282 7.500124138<br>
> >> Mo 7.721896396 7.156797182 5.926687354<br>
> >> S 7.739160210 8.974228888 4.353457824<br>
> >> S 7.739048493 8.974459743 7.500654977<br>
> >> Mo 7.722031044 1.675217921 5.926454615<br>
> >> S 7.739331052 3.492171149 4.352920557<br>
> >> S 7.738377057 3.492639347 7.499947690<br>
> >> Mo 9.304280720 4.416123626 5.927097215<br>
> >> S 9.321652087 6.232837357 4.353059451<br>
> >> S 9.321594176 6.234116854 7.500174405<br>
> >> Mo 10.887047440 7.156845127 5.926347019<br>
> >> S 10.903965611 8.974283787 4.353226240<br>
> >> S 10.903829602 8.974680010 7.500128022<br>
> >> C 5.700416780 4.960942076 11.705590151<br>
> >> C 5.786661978 6.354516349 11.705273773<br>
> >> C 7.046391983 6.956535202 11.705217371<br>
> >> C 8.203237318 6.173116561 11.705190411<br>
> >> C 8.099168585 4.780492709 11.705023203<br>
> >> C 6.846678887 4.164104064 11.704869934<br>
> >> Cl 4.129012811 4.204270654 11.705957792<br>
> >> H 4.877613854 6.955359406 11.704377918<br>
> >> H 7.118320846 8.046628444 11.704165169<br>
> >> H 9.184749419 6.647034640 11.704328004<br>
> >> H 8.998646725 4.161998637 11.704137157<br>
> >> H 6.757143341 3.077849963 11.704290956<br>
> >> K_POINTS automatic<br>
> >><br>
> >> 1 1 1 1 1 1<br>
> ><br>
> >*****************************<wbr>***************************<br>
> >- Article premier - Les hommes naissent et demeurent<br>
> >libres et ??gaux en droits. Les distinctions sociales<br>
> >ne peuvent ??tre fond??es que sur l'utilit?? commune<br>
> >- Article 2 - Le but de toute association politique<br>
> >est la conservation des droits naturels et<br>
> >imprescriptibles de l'homme. Ces droits sont la libert??,<br>
> >la propri??t??, la s??ret?? et la r??sistance ? l'oppression.<br>
> >*****************************<wbr>***************************<br>
> ><br>
> >? ? ? Giuseppe Mattioli<br>
> >? ? ? CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
> >? ? ? v. Salaria Km 29,300 - C.P. 10<br>
> >? ? ? I 00015 - Monterotondo Stazione (RM), Italy<br>
> >? ? ? Tel + 39 06 90672342 - Fax +39 06 90672316<br>
> >? ? ? E-mail: < <a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a> ><br>
> >? ? ? <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
> >? ? ? ResearcherID: F-6308-2012<br>
> ><br>
> >_____________________________<wbr>__________________<br>
> >Pw_forum mailing list<br>
> ><a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> ><a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
<br>
******************************<wbr>**************************<br>
- Article premier - Les hommes naissent et demeurent<br>
libres et ?gaux en droits. Les distinctions sociales<br>
ne peuvent ?tre fond?es que sur l'utilit? commune<br>
- Article 2 - Le but de toute association politique<br>
est la conservation des droits naturels et<br>
imprescriptibles de l'homme. Ces droits sont la libert?,<br>
la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
******************************<wbr>**************************<br>
<br>
Giuseppe Mattioli<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
v. Salaria Km 29,300 - C.P. 10<br>
I 00015 - Monterotondo Stazione (RM), Italy<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
<a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
ResearcherID: F-6308-2012<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 9<br>
Date: Fri, 24 Feb 2017 22:24:09 +0530<br>
From: Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
Subject: [Pw_forum] Error in routine phq_readin (5010)<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAPLukqnvyHp5vqp_eyeD-+jaF9J=<a href="mailto:GPWSDMd8VxeWeK57V5rqJg@mail.gmail.com"><wbr>GPWSDMd8VxeWeK57V5rqJg@mail.<wbr>gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
<br>
I am trying to run the ph.x code for my system in espress0-5.0.3, but the<br>
code stops with the following error code:<br>
<br>
<br>
<br>
<br>
<br>
<br>
* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%<br>
Error in routine phq_readin (5010): reading inputph<br>
namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%*<br>
<br>
<br>
Following is my input:<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
*phonon &INPUTPH outdir = './tmp'<br>
, prefix = 'In4' , ldisp =<br>
.true., dvscf_star%pat = .true. , recover<br>
= .false. , qplot = .false. ,<br>
q2d = .false. , q_in_band_form = .true. ,<br>
amass(1) = 114.82, iverbosity = 1,<br>
tr2_ph = 1e-10 , alpha_mix(1) = 0.7<br>
, nk1 = 31 , nk2 = 31<br>
, nk3 = 1 , k1 = 0<br>
, k2 = 0 , k3 = 0<br>
, nq1 = 5 , nq2 = 5<br>
, nq3 = 1 , /1.0 0.0 0.0 *<br>
<br>
Can anyone please help me with the above error message ?<br>
Thanks you.<br>
<br>
Sunetra.<br>
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Message: 10<br>
Date: Fri, 24 Feb 2017 20:12:20 +0300<br>
From: Semen Yesylevskyy <<a href="mailto:yesint@mail.ru">yesint@mail.ru</a>><br>
Subject: Re: [Pw_forum] All Lowdin charges are zero<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:1487956340.931890638@f149.i.mail.ru">1487956340.931890638@f149.i.<wbr>mail.ru</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Giuseppe,<br>
Thank you very much, now it is finally clear for me!<br>
Indeed I used PPs from "official" site. I had no idea that they may not contain some crucial pieces of information like wavefucntions.<br>
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.<br>
Are there any databases of pre-computed PPs with pseudowavefunctions included for H,C,Cl,S,Mo atoms?<br>
<br>
Sincerely,<br>
Semen<br>
<br>
<br>
>???????, 24 ??????? 2017, 18:40 +02:00 ?? Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><wbr>:<br>
><br>
><br>
>Dear Semen<br>
>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<br>
>your-path-to Espresso-6.0/atomic/Doc/<wbr>pseudo-gen.pdf<br>
>and some of the references contained therein.<br>
>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<br>
>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<br>
>regarding the generation and usage of several kinds of pseudopotential.<br>
><br>
>In your case, the optimized norm-conserving Vanderbilt's pseudopotentials (ONCV PPs) downloaded from this database<br>
><a href="http://www.quantum-simulation.org/potentials/sg15_oncv/" rel="noreferrer" target="_blank">http://www.quantum-<wbr>simulation.org/potentials/<wbr>sg15_oncv/</a><br>
>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<br>
>orbitals and the Lowdin partition of valence charge.<br>
><br>
>If you want to use such PPs you should<br>
><br>
>a) download and install the Hamann's code<br>
><br>
>b) re-generate the same PPs by yourself with the input you find in the header at the beginning of the PP file<br>
><br>
>And this was explained by Lorenzo Paulatto in the old thread mentioned in my previous mail.<br>
>?<br>
>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<br>
>to try to find whether there is anybody who can do this work for you...:-)<br>
>HTH<br>
>Giuseppe<br>
><br>
>On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote:<br>
>> Dear Giuseppe,<br>
>> Thank you for quick reply, but I hardly understand the terms and local moonspeak because I'm using Quantum Espresso for few days only.<br>
>> 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<br>
>> 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<br>
>> extensively and the only thing which I've found is the following: 1) do optimization with pw.x<br>
>> 2) do scf with pw.x<br>
>> 3) run projwfc.x<br>
>><br>
>> That is what I did without success...<br>
>><br>
>> Sincerely,<br>
>> Dr. Semen Yesylevskyy<br>
>><br>
>> Department of Physics of Biological Systems<br>
>> Institute of Physics of NAS of Ukraine<br>
>><br>
>> >??????????????, 24 ?????????????? 2017, 17:44 +02:00 ???? Giuseppe Mattioli < <a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a> >:<br>
>> ><br>
>> ><br>
>> ><br>
>> >Dear Colleague (please sign always the posts with name and affiliation)<br>
>> ><br>
>> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the Hamann's code to include them.<br>
>> >Look for this old thread in the QE forum<br>
>> ><br>
>> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc<br>
>> ><br>
>> >That should contain all you need to rebuild a PP with wfcs and to obtain Lowdin charges with projwfc.x<br>
>> ><br>
>> >HTH<br>
>> >Giuseppe<br>
>> ><br>
>> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:<br>
>> >> Dear All,<br>
>> >> 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<br>
>> >> 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<br>
>> >> not<br>
>> >> what I can expect:<br>
>> >><br>
>> >> Lowdin Charges:<br>
>> >> Atom # 1: total charge = 0.0000, s = 0.0000,<br>
>> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> >> Atom # 2: total charge = 0.0001, s = 0.0000,<br>
>> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> >> Atom # 3: total charge = 0.0001, s = 0.0000,<br>
>> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> >> Atom # 4: total charge = 0.0000, s = 0.0000,<br>
>> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> >> Atom # 5: total charge = 0.0001, s = 0.0000,<br>
>> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,<br>
>> >> Atom # 6: total charge = 0.0001, s = 0.0000,<br>
>> >><br>
>> >> ....<br>
>> >><br>
>> >> Could you please give me some advice of what I'm doing wrong?<br>
>> >><br>
>> >> ------------------------------<wbr>--<br>
>> >><br>
>> >> The projwcf input:<br>
>> >> &PROJWFC<br>
>> >><br>
>> >> prefix = './3cell-cb_scf' ,<br>
>> >> outdir = '.' ,<br>
>> >> ngauss = 0.1 ,<br>
>> >> DeltaE = 0.01 ,<br>
>> >><br>
>> >> /<br>
>> >><br>
>> >> ------------------------------<wbr>--<br>
>> >><br>
>> >> The scf input:<br>
>> >> &CONTROL<br>
>> >><br>
>> >> calculation = 'scf' ,<br>
>> >><br>
>> >> restart_mode = 'from_scratch' ,<br>
>> >><br>
>> >> outdir = '.' ,<br>
>> >> wfcdir = './tmp' ,<br>
>> >><br>
>> >> pseudo_dir = '.' ,<br>
>> >><br>
>> >> prefix = '3cell-cb_scf' ,<br>
>> >><br>
>> >> nstep = 1000 ,<br>
>> >><br>
>> >> tstress = .false. ,<br>
>> >><br>
>> >> /<br>
>> >> &SYSTEM<br>
>> >><br>
>> >> ibrav = 4 ,<br>
>> >><br>
>> >> A = 9.495 ,<br>
>> >> B = 9.495 ,<br>
>> >> C = 100.0 ,<br>
>> >><br>
>> >> cosAB = 0.5 ,<br>
>> >> cosAC = 0 ,<br>
>> >> cosBC = 0 ,<br>
>> >><br>
>> >> nat = 39,<br>
>> >><br>
>> >> ntyp = 5,<br>
>> >><br>
>> >> ecutwfc = 35 ,<br>
>> >> ecutrho = 140 ,<br>
>> >><br>
>> >> nosym = .true. ,<br>
>> >><br>
>> >> tot_charge = 0.000000 ,<br>
>> >><br>
>> >> /<br>
>> >> &ELECTRONS<br>
>> >><br>
>> >> electron_maxstep = 200 ,<br>
>> >> scf_must_converge = .false. ,<br>
>> >> diagonalization='cg' ,<br>
>> >><br>
>> >> /<br>
>> >> &IONS<br>
>> >><br>
>> >> ion_dynamics = 'bfgs' ,<br>
>> >><br>
>> >> /<br>
>> >><br>
>> >> ATOMIC_SPECIES<br>
>> >><br>
>> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf<br>
>> >><br>
>> >> S 32.06 S_pbe_v1.2.uspp.F.UPF<br>
>> >> C 12.011 C_pbe_v1.2.uspp.F.UPF<br>
>> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF<br>
>> >><br>
>> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF<br>
>> >><br>
>> >> ATOMIC_POSITIONS angstrom<br>
>> >> Mo 1.392123361 1.675146760 5.927158394<br>
>> >> S 1.409356288 3.492127081 4.353797199<br>
>> >> S 1.409009361 3.492914431 7.500696022<br>
>> >> Mo 2.974783806 4.416004278 5.927352435<br>
>> >> S 2.991861295 6.232688291 4.353114990<br>
>> >> S 2.991733615 6.233889787 7.500216780<br>
>> >> Mo 4.557309411 7.156655993 5.926482117<br>
>> >> S 4.574550104 8.974187415 4.353268832<br>
>> >> S 4.573865790 8.974308816 7.499997172<br>
>> >> Mo 4.556900653 1.675497042 5.926861427<br>
>> >> S 4.573955171 3.492114510 4.352949498<br>
>> >> S 4.574377417 3.492858021 7.500504130<br>
>> >> Mo 6.139333906 4.416035304 5.926363713<br>
>> >> S 6.156932316 6.232998289 4.352535948<br>
>> >> S 6.156651090 6.233324282 7.500124138<br>
>> >> Mo 7.721896396 7.156797182 5.926687354<br>
>> >> S 7.739160210 8.974228888 4.353457824<br>
>> >> S 7.739048493 8.974459743 7.500654977<br>
>> >> Mo 7.722031044 1.675217921 5.926454615<br>
>> >> S 7.739331052 3.492171149 4.352920557<br>
>> >> S 7.738377057 3.492639347 7.499947690<br>
>> >> Mo 9.304280720 4.416123626 5.927097215<br>
>> >> S 9.321652087 6.232837357 4.353059451<br>
>> >> S 9.321594176 6.234116854 7.500174405<br>
>> >> Mo 10.887047440 7.156845127 5.926347019<br>
>> >> S 10.903965611 8.974283787 4.353226240<br>
>> >> S 10.903829602 8.974680010 7.500128022<br>
>> >> C 5.700416780 4.960942076 11.705590151<br>
>> >> C 5.786661978 6.354516349 11.705273773<br>
>> >> C 7.046391983 6.956535202 11.705217371<br>
>> >> C 8.203237318 6.173116561 11.705190411<br>
>> >> C 8.099168585 4.780492709 11.705023203<br>
>> >> C 6.846678887 4.164104064 11.704869934<br>
>> >> Cl 4.129012811 4.204270654 11.705957792<br>
>> >> H 4.877613854 6.955359406 11.704377918<br>
>> >> H 7.118320846 8.046628444 11.704165169<br>
>> >> H 9.184749419 6.647034640 11.704328004<br>
>> >> H 8.998646725 4.161998637 11.704137157<br>
>> >> H 6.757143341 3.077849963 11.704290956<br>
>> >> K_POINTS automatic<br>
>> >><br>
>> >> 1 1 1 1 1 1<br>
>> ><br>
>> >*****************************<wbr>***************************<br>
>> >- Article premier - Les hommes naissent et demeurent<br>
>> >libres et ??gaux en droits. Les distinctions sociales<br>
>> >ne peuvent ??tre fond??es que sur l'utilit?? commune<br>
>> >- Article 2 - Le but de toute association politique<br>
>> >est la conservation des droits naturels et<br>
>> >imprescriptibles de l'homme. Ces droits sont la libert??,<br>
>> >la propri??t??, la s??ret?? et la r??sistance ? l'oppression.<br>
>> >*****************************<wbr>***************************<br>
>> ><br>
>> >? ? ? Giuseppe Mattioli<br>
>> >? ? ? CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
>> >? ? ? v. Salaria Km 29,300 - C.P. 10<br>
>> >? ? ? I 00015 - Monterotondo Stazione (RM), Italy<br>
>> >? ? ? Tel + 39 06 90672342 - Fax +39 06 90672316<br>
>> >? ? ? E-mail: < <a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a> ><br>
>> >? ? ? <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
>> >? ? ? ResearcherID: F-6308-2012<br>
>> ><br>
>> >_____________________________<wbr>__________________<br>
>> >Pw_forum mailing list<br>
>> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
>> > <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
><br>
>*****************************<wbr>***************************<br>
>- Article premier - Les hommes naissent et demeurent<br>
>libres et ?gaux en droits. Les distinctions sociales<br>
>ne peuvent ?tre fond?es que sur l'utilit? commune<br>
>- Article 2 - Le but de toute association politique<br>
>est la conservation des droits naturels et<br>
>imprescriptibles de l'homme. Ces droits sont la libert?,<br>
>la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
>*****************************<wbr>***************************<br>
><br>
>???Giuseppe Mattioli<br>
>???CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
>???v. Salaria Km 29,300 - C.P. 10<br>
>???I 00015 - Monterotondo Stazione (RM), Italy<br>
>???Tel + 39 06 90672342 - Fax +39 06 90672316<br>
>???E-mail: < <a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a> ><br>
>??? <a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/<wbr>staff/giuseppe-mattioli/</a><br>
>???ResearcherID: F-6308-2012<br>
><br>
>_____________________________<wbr>__________________<br>
>Pw_forum mailing list<br>
><a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
><a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
<br>
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------------------------------<br>
<br>
Message: 11<br>
Date: Fri, 24 Feb 2017 17:52:12 +0000<br>
From: Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk">ellf@leeds.ac.uk</a>><br>
Subject: Re: [Pw_forum] Error in routine phq_readin (5010)<br>
To: "<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:DB5PR0301MB1942C6C26EFCC7F825E5EC649E520@DB5PR0301MB1942.eurprd03.prod.outlook.com">DB5PR0301MB1942C6C26EFCC7F825<wbr>E5EC649E520@DB5PR0301MB1942.<wbr>eurprd03.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Sunetra,<br>
<br>
<br>
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:<br>
<br>
<br>
nq2 = 5 ,<br>
nq3 = 1 <------------<br>
/<br>
1.0 0.0 0.0<br>
<br>
<br>
If that doesn't work other input fields might not be correct..<br>
<br>
<br>
Kindest regards,<br>
<br>
Louis<br>
<br>
______________________________<wbr>__<br>
From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on behalf of Sunetra Das <<a href="mailto:sunetra.das.88@gmail.com">sunetra.das.88@gmail.com</a>><br>
Sent: 24 February 2017 16:54:09<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Subject: [Pw_forum] Error in routine phq_readin (5010)<br>
<br>
Hello all,<br>
<br>
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:<br>
<br>
<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%<br>
Error in routine phq_readin (5010):<br>
reading inputph namelist<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<wbr>%%%%%%%%%%%%%%%%%%<br>
<br>
<br>
Following is my input:<br>
<br>
phonon<br>
&INPUTPH<br>
outdir = './tmp' ,<br>
prefix = 'In4' ,<br>
ldisp = .true.,<br>
dvscf_star%pat = .true. ,<br>
recover = .false. ,<br>
qplot = .false. ,<br>
q2d = .false. ,<br>
q_in_band_form = .true. ,<br>
amass(1) = 114.82,<br>
iverbosity = 1,<br>
tr2_ph = 1e-10 ,<br>
alpha_mix(1) = 0.7 ,<br>
nk1 = 31 ,<br>
nk2 = 31 ,<br>
nk3 = 1 ,<br>
k1 = 0 ,<br>
k2 = 0 ,<br>
k3 = 0 ,<br>
nq1 = 5 ,<br>
nq2 = 5 ,<br>
nq3 = 1 ,<br>
/<br>
1.0 0.0 0.0<br>
<br>
<br>
Can anyone please help me with the above error message ?<br>
Thanks you.<br>
<br>
Sunetra.<br>
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<br>
------------------------------<br>
<br>
Message: 12<br>
Date: Fri, 24 Feb 2017 19:03:59 +0100 (CET)<br>
From: Andrea Ferretti <<a href="mailto:andrea.ferretti@unimore.it">andrea.ferretti@unimore.it</a>><br>
Subject: [Pw_forum] MaX user portal and newsletter<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <alpine.DEB.2.10.<wbr>1702241902410.11726@potzie><br>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed<br>
<br>
<br>
<br>
<br>
Dear All,<br>
<br>
this email is to inform that the MaX user portal, offering services also<br>
connected to Quantum ESPRESSO and its community, is now ready. Everyone can<br>
subscribe. For further information please have a look at the MaX<br>
newsletter<br>
(link below).<br>
<br>
take care<br>
Andrea<br>
<br>
==============================<wbr>====<br>
<br>
MaX User Portal ready<br>
<br>
Six services are now up and r...</blockquote></div>