Dear Giuseppe, Thank you very much, now it is finally clear for me! Indeed I used PPs from "official" site. I had no idea that they may not contain some crucial pieces of information like wavefucntions. I really don't want to regenerate them at this stage because this work is a small side project which does not justify going so deep into the field. Are there any databases of pre-computed PPs with pseudowavefunctions included for H,C,Cl,S,Mo atoms?
Sincerely, Semen >Пятница, 24 февраля 2017, 18:40 +02:00 от Giuseppe Mattioli ><[email protected]>: > > >Dear Semen >I suppose that you know what a pseudopotential is and how does it work... If >you don't, I recommend first that you read this guide >your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf >and some of the references contained therein. >Pseudopotentials can be generated by using the ld1.x (aka atomic) code >embedded in the QE distributuin, but they are more often imported from various >databases that are NOT part of the distribution, and are in such case used "at >your own risk", even if there is a diffuse knowledge between QE users >regarding the generation and usage of several kinds of pseudopotential. > >In your case, the optimized norm-conserving Vanderbilt's pseudopotentials >(ONCV PPs) downloaded from this database >http://www.quantum-simulation.org/potentials/sg15_oncv/ >do not contain the pseudowavefunctions, so projwfc.x does not find a suitable >set of atomic orbitals to calculate the atomic projection of Kohn-Sham >orbitals and the Lowdin partition of valence charge. > >If you want to use such PPs you should > >a) download and install the Hamann's code > >b) re-generate the same PPs by yourself with the input you find in the header >at the beginning of the PP file > >And this was explained by Lorenzo Paulatto in the old thread mentioned in my >previous mail. > >I suppose that it is not exactly easy for a newbie of PP generation, so for >the time being I can only suggest you to use different pseudopotentials, or >to try to find whether there is anybody who can do this work for you...:-) >HTH >Giuseppe > >On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote: >> Dear Giuseppe, >> Thank you for quick reply, but I hardly understand the terms and local >> moonspeak because I'm using Quantum Espresso for few days only. >> I understand that some information for projwfc is missed but the topic you >> mentioned does not give me any clue of what should I do with my input to >> have it. Could you please point me to some step-by-step instruction of what >> should I do to get correct Lowdin charges? I googled for this >> extensively and the only thing which I've found is the following: 1) do >> optimization with pw.x >> 2) do scf with pw.x >> 3) run projwfc.x >> >> That is what I did without success... >> >> Sincerely, >> Dr. Semen Yesylevskyy >> >> Department of Physics of Biological Systems >> Institute of Physics of NAS of Ukraine >> >> >ÐÑÑниÑа, 24 ÑевÑÐ°Ð»Ñ 2017, 17:44 +02:00 Ð¾Ñ Giuseppe Mattioli >> >< [email protected] >: >> > >> > >> > >> >Dear Colleague (please sign always the posts with name and affiliation) >> > >> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the >> >Hamann's code to include them. >> >Look for this old thread in the QE forum >> > >> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc >> > >> >That should contain all you need to rebuild a PP with wfcs and to obtain >> >Lowdin charges with projwfc.x >> > >> >HTH >> >Giuseppe >> > >> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote: >> >> Dear All, >> >> I'm new to QE so please forgive if I'm missing something very obvious. >> >> I'm trying to study the charge transfer between organic molecules and MoS2 >> >> monolayer. I optimized the system, did an scf and then tried to get >> >> Lowdin charges with projwcf. However, all charges are almost zero which is >> >> not >> >> what I can expect: >> >> >> >> Lowdin Charges: >> >> Atom # 1: total charge = 0.0000, s = 0.0000, >> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= >> >> 0.0000, py= 0.0000, >> >> Atom # 2: total charge = 0.0001, s = 0.0000, >> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= >> >> 0.0000, py= 0.0000, >> >> Atom # 3: total charge = 0.0001, s = 0.0000, >> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= >> >> 0.0000, py= 0.0000, >> >> Atom # 4: total charge = 0.0000, s = 0.0000, >> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= >> >> 0.0000, py= 0.0000, >> >> Atom # 5: total charge = 0.0001, s = 0.0000, >> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= >> >> 0.0000, py= 0.0000, >> >> Atom # 6: total charge = 0.0001, s = 0.0000, >> >> >> >> .... >> >> >> >> Could you please give me some advice of what I'm doing wrong? >> >> >> >> -------------------------------- >> >> >> >> The projwcf input: >> >> &PROJWFC >> >> >> >> prefix = './3cell-cb_scf' , >> >> outdir = '.' , >> >> ngauss = 0.1 , >> >> DeltaE = 0.01 , >> >> >> >> / >> >> >> >> -------------------------------- >> >> >> >> The scf input: >> >> &CONTROL >> >> >> >> calculation = 'scf' , >> >> >> >> restart_mode = 'from_scratch' , >> >> >> >> outdir = '.' , >> >> wfcdir = './tmp' , >> >> >> >> pseudo_dir = '.' , >> >> >> >> prefix = '3cell-cb_scf' , >> >> >> >> nstep = 1000 , >> >> >> >> tstress = .false. , >> >> >> >> / >> >> &SYSTEM >> >> >> >> ibrav = 4 , >> >> >> >> A = 9.495 , >> >> B = 9.495 , >> >> C = 100.0 , >> >> >> >> cosAB = 0.5 , >> >> cosAC = 0 , >> >> cosBC = 0 , >> >> >> >> nat = 39, >> >> >> >> ntyp = 5, >> >> >> >> ecutwfc = 35 , >> >> ecutrho = 140 , >> >> >> >> nosym = .true. , >> >> >> >> tot_charge = 0.000000 , >> >> >> >> / >> >> &ELECTRONS >> >> >> >> electron_maxstep = 200 , >> >> scf_must_converge = .false. , >> >> diagonalization='cg' , >> >> >> >> / >> >> &IONS >> >> >> >> ion_dynamics = 'bfgs' , >> >> >> >> / >> >> >> >> ATOMIC_SPECIES >> >> >> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf >> >> >> >> S 32.06 S_pbe_v1.2.uspp.F.UPF >> >> C 12.011 C_pbe_v1.2.uspp.F.UPF >> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF >> >> >> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF >> >> >> >> ATOMIC_POSITIONS angstrom >> >> Mo 1.392123361 1.675146760 5.927158394 >> >> S 1.409356288 3.492127081 4.353797199 >> >> S 1.409009361 3.492914431 7.500696022 >> >> Mo 2.974783806 4.416004278 5.927352435 >> >> S 2.991861295 6.232688291 4.353114990 >> >> S 2.991733615 6.233889787 7.500216780 >> >> Mo 4.557309411 7.156655993 5.926482117 >> >> S 4.574550104 8.974187415 4.353268832 >> >> S 4.573865790 8.974308816 7.499997172 >> >> Mo 4.556900653 1.675497042 5.926861427 >> >> S 4.573955171 3.492114510 4.352949498 >> >> S 4.574377417 3.492858021 7.500504130 >> >> Mo 6.139333906 4.416035304 5.926363713 >> >> S 6.156932316 6.232998289 4.352535948 >> >> S 6.156651090 6.233324282 7.500124138 >> >> Mo 7.721896396 7.156797182 5.926687354 >> >> S 7.739160210 8.974228888 4.353457824 >> >> S 7.739048493 8.974459743 7.500654977 >> >> Mo 7.722031044 1.675217921 5.926454615 >> >> S 7.739331052 3.492171149 4.352920557 >> >> S 7.738377057 3.492639347 7.499947690 >> >> Mo 9.304280720 4.416123626 5.927097215 >> >> S 9.321652087 6.232837357 4.353059451 >> >> S 9.321594176 6.234116854 7.500174405 >> >> Mo 10.887047440 7.156845127 5.926347019 >> >> S 10.903965611 8.974283787 4.353226240 >> >> S 10.903829602 8.974680010 7.500128022 >> >> C 5.700416780 4.960942076 11.705590151 >> >> C 5.786661978 6.354516349 11.705273773 >> >> C 7.046391983 6.956535202 11.705217371 >> >> C 8.203237318 6.173116561 11.705190411 >> >> C 8.099168585 4.780492709 11.705023203 >> >> C 6.846678887 4.164104064 11.704869934 >> >> Cl 4.129012811 4.204270654 11.705957792 >> >> H 4.877613854 6.955359406 11.704377918 >> >> H 7.118320846 8.046628444 11.704165169 >> >> H 9.184749419 6.647034640 11.704328004 >> >> H 8.998646725 4.161998637 11.704137157 >> >> H 6.757143341 3.077849963 11.704290956 >> >> K_POINTS automatic >> >> >> >> 1 1 1 1 1 1 >> > >> >******************************************************** >> >- Article premier - Les hommes naissent et demeurent >> >libres et égaux en droits. Les distinctions sociales >> >ne peuvent être fondées que sur l'utilité commune >> >- Article 2 - Le but de toute association politique >> >est la conservation des droits naturels et >> >imprescriptibles de l'homme. Ces droits sont la liberté, >> >la propriété, la sûreté et la résistance à l'oppression. >> >******************************************************** >> > >> >   Giuseppe Mattioli >> >   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >> >   v. Salaria Km 29,300 - C.P. 10 >> >   I 00015 - Monterotondo Stazione (RM), Italy >> >   Tel + 39 06 90672342 - Fax +39 06 90672316 >> >   E-mail: < [email protected] > >> >   http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ >> >   ResearcherID: F-6308-2012 >> > >> >_______________________________________________ >> >Pw_forum mailing list >> > [email protected] >> > http://pwscf.org/mailman/listinfo/pw_forum > >******************************************************** >- Article premier - Les hommes naissent et demeurent >libres et égaux en droits. Les distinctions sociales >ne peuvent être fondées que sur l'utilité commune >- Article 2 - Le but de toute association politique >est la conservation des droits naturels et >imprescriptibles de l'homme. Ces droits sont la liberté, >la propriété, la sûreté et la résistance à l'oppression. >******************************************************** > > Giuseppe Mattioli > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > v. Salaria Km 29,300 - C.P. 10 > I 00015 - Monterotondo Stazione (RM), Italy > Tel + 39 06 90672342 - Fax +39 06 90672316 > E-mail: < [email protected] > > http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > ResearcherID: F-6308-2012 > >_______________________________________________ >Pw_forum mailing list >[email protected] >http://pwscf.org/mailman/listinfo/pw_forum
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