[Pw_forum] All Lowdin charges are zero
Semen Yesylevskyy
yesint at mail.ru
Fri Feb 24 18:12:20 CET 2017
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 <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.
>
>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
>> >
>> >********************************************************
>> >- 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
>> >
>> >_______________________________________________
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>> > 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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