[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
> 
> >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
> >> 
> >> >Пятница, 24 февраля 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
> >> >
> >> >_______________________________________________
> >> >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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