[Pw_forum] All Lowdin charges are zero
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Mon Feb 27 11:01:04 CET 2017
Dear Semen
Flicking through the QE pseudopotential page
http://www.quantum-espresso.org/pseudopotentials/
among many other, I've found these ones that should suitable for your purpose (but you should always check with the appropriate convergence tests...).
Ultrasoft PPs (suggested cutoffs: ecutwfc=40.0, ecutrho=320.0~400.0)
Mo.pbe-spn-rrkjus_psl.0.2.UPF
S.pbe-n-rrkjus_psl.0.1.UPF
C.pbe-n-rrkjus_psl.0.1.UPF
H.pbe-rrkjus_psl.0.1.UPF
Cl.pbe-n-rrkjus_psl.0.1.UPF
HTH
Giuseppe
On Friday, February 24, 2017 08:12:20 PM Semen Yesylevskyy wrote:
> 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
>
> >ПÑтница, 24 Ñ„ÐµÐ²Ñ€Ð°Ð»Ñ 2017, 18:40 +02:00 от Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>:
> >
> >
> >Dear Semen
> >I suppose that you know what a pseudopotential is and how does it work... If you don't, I recommend first that you read this guide
> >your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf
> >and some of the references contained therein.
> >Pseudopotentials can be generated by using the ld1.x (aka atomic) code embedded in the QE distributuin, but they are more often imported from
> >various databases that are NOT part of the distribution, and are in such case used "at your own risk", even if there is a diffuse knowledge
> >between QE users regarding the generation and usage of several kinds of pseudopotential.
> >
> >In your case, the optimized norm-conserving Vanderbilt's pseudopotentials (ONCV PPs) downloaded from this database
> >http://www.quantum-simulation.org/potentials/sg15_oncv/
> >do not contain the pseudowavefunctions, so projwfc.x does not find a suitable set of atomic orbitals to calculate the atomic projection of
> >Kohn-Sham orbitals and the Lowdin partition of valence charge.
> >
> >If you want to use such PPs you should
> >
> >a) download and install the Hamann's code
> >
> >b) re-generate the same PPs by yourself with the input you find in the header at the beginning of the PP file
> >
> >And this was explained by Lorenzo Paulatto in the old thread mentioned in my previous mail.
> >Â
> >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
> >>
> >> >ßÑÂтýøцð, 24 фõòрðûѠ2017, 17:44 +02:00 þт Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it >:
> >> >
> >> >
> >> >
> >> >Dear Colleague (please sign always the posts with name and affiliation)
> >> >
> >> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the Hamann's code to include them.
> >> >Look for this old thread in the QE forum
> >> >
> >> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc
> >> >
> >> >That should contain all you need to rebuild a PP with wfcs and to obtain Lowdin charges with projwfc.x
> >> >
> >> >HTH
> >> >Giuseppe
> >> >
> >> >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote:
> >> >> Dear All,
> >> >> I'm new to QE so please forgive if I'm missing something very obvious. I'm trying to study the charge transfer between organic molecules and
> >> >> MoS2
> >> >> monolayer. I optimized the system, did an scf and then tried to get Lowdin charges with projwcf. However, all charges are almost zero which is
> >> >> not
> >> >> what I can expect:
> >> >>
> >> >> Lowdin Charges:
> >> >> Atom # 1: total charge = 0.0000, s = 0.0000,
> >> >> Atom # 1: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,
> >> >> Atom # 2: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,
> >> >> Atom # 3: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,
> >> >> Atom # 4: total charge = 0.0000, s = 0.0000,
> >> >> Atom # 4: total charge = 0.0000, p = 0.0000, pz= 0.0000, px= 0.0000, py= 0.0000,
> >> >> Atom # 5: total charge = 0.0001, s = 0.0000,
> >> >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0.0000, px= 0.0000, py= 0.0000,
> >> >> Atom # 6: total charge = 0.0001, s = 0.0000,
> >> >>
> >> >> ....
> >> >>
> >> >> Could you please give me some advice of what I'm doing wrong?
> >> >>
> >> >> --------------------------------
> >> >>
> >> >> The projwcf input:
> >> >> &PROJWFC
> >> >>
> >> >> prefix = './3cell-cb_scf' ,
> >> >> outdir = '.' ,
> >> >> ngauss = 0.1 ,
> >> >> DeltaE = 0.01 ,
> >> >>
> >> >> /
> >> >>
> >> >> --------------------------------
> >> >>
> >> >> The scf input:
> >> >> &CONTROL
> >> >>
> >> >> calculation = 'scf' ,
> >> >>
> >> >> restart_mode = 'from_scratch' ,
> >> >>
> >> >> outdir = '.' ,
> >> >> wfcdir = './tmp' ,
> >> >>
> >> >> pseudo_dir = '.' ,
> >> >>
> >> >> prefix = '3cell-cb_scf' ,
> >> >>
> >> >> nstep = 1000 ,
> >> >>
> >> >> tstress = .false. ,
> >> >>
> >> >> /
> >> >> &SYSTEM
> >> >>
> >> >> ibrav = 4 ,
> >> >>
> >> >> A = 9.495 ,
> >> >> B = 9.495 ,
> >> >> C = 100.0 ,
> >> >>
> >> >> cosAB = 0.5 ,
> >> >> cosAC = 0 ,
> >> >> cosBC = 0 ,
> >> >>
> >> >> nat = 39,
> >> >>
> >> >> ntyp = 5,
> >> >>
> >> >> ecutwfc = 35 ,
> >> >> ecutrho = 140 ,
> >> >>
> >> >> nosym = .true. ,
> >> >>
> >> >> tot_charge = 0.000000 ,
> >> >>
> >> >> /
> >> >> &ELECTRONS
> >> >>
> >> >> electron_maxstep = 200 ,
> >> >> scf_must_converge = .false. ,
> >> >> diagonalization='cg' ,
> >> >>
> >> >> /
> >> >> &IONS
> >> >>
> >> >> ion_dynamics = 'bfgs' ,
> >> >>
> >> >> /
> >> >>
> >> >> ATOMIC_SPECIES
> >> >>
> >> >> Mo 95.96 Mo_ONCV_PBE-1.0.upf
> >> >>
> >> >> S 32.06 S_pbe_v1.2.uspp.F.UPF
> >> >> C 12.011 C_pbe_v1.2.uspp.F.UPF
> >> >> H 1.008 H.pbe-rrkjus_psl.0.1.UPF
> >> >>
> >> >> Cl 35.45 cl_pbe_v1.4.uspp.F.UPF
> >> >>
> >> >> ATOMIC_POSITIONS angstrom
> >> >> Mo 1.392123361 1.675146760 5.927158394
> >> >> S 1.409356288 3.492127081 4.353797199
> >> >> S 1.409009361 3.492914431 7.500696022
> >> >> Mo 2.974783806 4.416004278 5.927352435
> >> >> S 2.991861295 6.232688291 4.353114990
> >> >> S 2.991733615 6.233889787 7.500216780
> >> >> Mo 4.557309411 7.156655993 5.926482117
> >> >> S 4.574550104 8.974187415 4.353268832
> >> >> S 4.573865790 8.974308816 7.499997172
> >> >> Mo 4.556900653 1.675497042 5.926861427
> >> >> S 4.573955171 3.492114510 4.352949498
> >> >> S 4.574377417 3.492858021 7.500504130
> >> >> Mo 6.139333906 4.416035304 5.926363713
> >> >> S 6.156932316 6.232998289 4.352535948
> >> >> S 6.156651090 6.233324282 7.500124138
> >> >> Mo 7.721896396 7.156797182 5.926687354
> >> >> S 7.739160210 8.974228888 4.353457824
> >> >> S 7.739048493 8.974459743 7.500654977
> >> >> Mo 7.722031044 1.675217921 5.926454615
> >> >> S 7.739331052 3.492171149 4.352920557
> >> >> S 7.738377057 3.492639347 7.499947690
> >> >> Mo 9.304280720 4.416123626 5.927097215
> >> >> S 9.321652087 6.232837357 4.353059451
> >> >> S 9.321594176 6.234116854 7.500174405
> >> >> Mo 10.887047440 7.156845127 5.926347019
> >> >> S 10.903965611 8.974283787 4.353226240
> >> >> S 10.903829602 8.974680010 7.500128022
> >> >> C 5.700416780 4.960942076 11.705590151
> >> >> C 5.786661978 6.354516349 11.705273773
> >> >> C 7.046391983 6.956535202 11.705217371
> >> >> C 8.203237318 6.173116561 11.705190411
> >> >> C 8.099168585 4.780492709 11.705023203
> >> >> C 6.846678887 4.164104064 11.704869934
> >> >> Cl 4.129012811 4.204270654 11.705957792
> >> >> H 4.877613854 6.955359406 11.704377918
> >> >> H 7.118320846 8.046628444 11.704165169
> >> >> H 9.184749419 6.647034640 11.704328004
> >> >> H 8.998646725 4.161998637 11.704137157
> >> >> H 6.757143341 3.077849963 11.704290956
> >> >> K_POINTS automatic
> >> >>
> >> >> 1 1 1 1 1 1
> >> >
> >> >********************************************************
> >> >- Article premier - Les hommes naissent et demeurent
> >> >libres et 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.
> >> >********************************************************
> >> >
> >> >Â Â Â Giuseppe Mattioli
> >> >Â Â Â CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >> >Â Â Â v. Salaria Km 29,300 - C.P. 10
> >> >Â Â Â I 00015 - Monterotondo Stazione (RM), Italy
> >> >Â Â Â Tel + 39 06 90672342 - Fax +39 06 90672316
> >> >Â Â Â E-mail: < giuseppe.mattioli at ism.cnr.it >
> >> >Â Â Â http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
> >> >Â Â Â ResearcherID: F-6308-2012
> >> >
> >> >_______________________________________________
> >> >Pw_forum mailing list
> >> >
> >> > Pw_forum at pwscf.org
> >> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> >********************************************************
> >- Article premier - Les hommes naissent et demeurent
> >libres et 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.
> >********************************************************
> >
> >Â Â Â Giuseppe Mattioli
> >Â Â Â CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> >Â Â Â v. Salaria Km 29,300 - C.P. 10
> >Â Â Â I 00015 - Monterotondo Stazione (RM), Italy
> >Â Â Â Tel + 39 06 90672342 - Fax +39 06 90672316
> >Â Â Â E-mail: < giuseppe.mattioli at ism.cnr.it >
> >Â Â Â http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
> >Â Â Â ResearcherID: F-6308-2012
> >
> >_______________________________________________
> >Pw_forum mailing list
> >Pw_forum at pwscf.org
> >http://pwscf.org/mailman/listinfo/pw_forum
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et 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: <giuseppe.mattioli at ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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