<HTML><BODY>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><blockquote style="border-left:1px solid #0857A6; margin:10px; padding:0 0 0 10px;">
Пятница, 24 февраля 2017, 18:40 +02:00 от Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it>:<br>
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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/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/" target="_blank">http://www.quantum-simulation.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>
> >ÐÑÑниÑа, 24 ÑевÑÐ°Ð»Ñ 2017, 17:44 +02:00 Ð¾Ñ 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>
> >> --------------------------------<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>
> >> --------------------------------<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>
> >********************************************************<br>
> >- Article premier - Les hommes naissent et demeurent<br>
> >libres et égaux en droits. Les distinctions sociales<br>
> >ne peuvent être fondées que sur l'utilité 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 liberté,<br>
> >la propriété, la sûreté et la résistance à l'oppression.<br>
> >********************************************************<br>
> ><br>
> >Â Â Â Giuseppe Mattioli<br>
> >Â Â Â CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
> >Â Â Â v. Salaria Km 29,300 - C.P. 10<br>
> >Â Â Â I 00015 - Monterotondo Stazione (RM), Italy<br>
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> >Â Â Â ResearcherID: F-6308-2012<br>
> ><br>
> >_______________________________________________<br>
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********************************************************<br>
- Article premier - Les hommes naissent et demeurent<br>
libres et égaux en droits. Les distinctions sociales<br>
ne peuvent être fondées que sur l'utilité 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 liberté,<br>
la propriété, la sûreté et la résistance à l'oppression.<br>
********************************************************<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 <span class="js-phone-number">+39 06 90672316</span> <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/" target="_blank">http://www.ism.cnr.it/en/staff/giuseppe-mattioli/</a><br>
ResearcherID: F-6308-2012<br>
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