[Pw_forum] All Lowdin charges are zero
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Fri Feb 24 17:40:55 CET 2017
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
>
> >ПÑтница, 24 Ñ„ÐµÐ²Ñ€Ð°Ð»Ñ 2017, 17:44 +02:00 от 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
> >
> >********************************************************
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> >********************************************************
> >
> >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
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> >
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********************************************************
- 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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