Re: [Pw_forum] All Lowdin charges are zero

[Giuseppe Mattioli]

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 
> >:
> >
> >
> >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
> >> 
> >> >Пятница, 24 февраля 2017, 17:44 
> >> >+02:00 от Giuseppe Mattioli < giuseppe.matti...@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., s =  0.,
> >> >>  Atom #   1: total charge =   0., p =  0., pz=  

Re: [Pw_forum] All Lowdin charges are zero

[Semen Yesylevskyy]

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 
>:
>
>
>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.matti...@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., s =  0.,
>> >>  Atom #   1: total charge =   0., p =  0., pz=  0., px=  
>> >> 0., py=  0.,
>> >>  Atom #   2: total charge =   0.0001, s =  0.,
>> >>  Atom #   2: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> >> 0., py=  0.,
>> >>  Atom #   3: total charge =   0.0001, s =  0.,
>> >>  Atom #   3: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> >> 0., py=  0.,
>> >>  Atom #   4: total charge =   0., s =  0.,
>> >>  Atom #   4: total charge =   0., p =  0., pz=  0., px=  
>> >> 0., py=  0.,
>> >>  Atom #   5: total charge =   0.0001, s =  0.,
>> >>  Atom #   5: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> >> 0., py=  0.,
>> >>  Atom #   6: total charge =   0.0001, s =  0.,
>> >> 
>> >> 
>> >> 
>> >> Could you please give 

Re: [Pw_forum] All Lowdin charges are zero

[Giuseppe Mattioli]

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 
> >:
> >
> >
> >
> >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., s =  0.,
> >>  Atom #   1: total charge =   0., p =  0., pz=  0., px=  
> >> 0., py=  0.,
> >>  Atom #   2: total charge =   0.0001, s =  0.,
> >>  Atom #   2: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> >> 0., py=  0.,
> >>  Atom #   3: total charge =   0.0001, s =  0.,
> >>  Atom #   3: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> >> 0., py=  0.,
> >>  Atom #   4: total charge =   0., s =  0.,
> >>  Atom #   4: total charge =   0., p =  0., pz=  0., px=  
> >> 0., py=  0.,
> >>  Atom #   5: total charge =   0.0001, s =  0.,
> >>  Atom #   5: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> >> 0., py=  0.,
> >>  Atom #   6: total charge =   0.0001, s =  0.,
> >> 
> >> 
> >> 
> >> Could you please give me some advice of what I'm doing wrong?
> >> 
> >> 
> >> 
> >> The projwcf input:
> >>  
> >>  
> >>   prefix = './3cell-cb_scf' ,
> >>   outdir = '.' ,
> >>   ngauss = 0.1 ,
> >>   DeltaE = 0.01 ,
> >>  
> >>  /
> >> 
> >> 
> >> 
> >> The scf input:
> >>  
> >>  
> >>  calculation = 'scf' ,
> >> 
> >> restart_mode = 'from_scratch' ,
> >> 
> >>   outdir = '.' ,
> >>   wfcdir = './tmp' ,
> >>   
> >>  

Re: [Pw_forum] All Lowdin charges are zero

[Semen Yesylevskyy]

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 
>:
>
>
>
>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., s =  0.,
>>  Atom #   1: total charge =   0., p =  0., pz=  0., px=  
>> 0., py=  0.,
>>  Atom #   2: total charge =   0.0001, s =  0.,
>>  Atom #   2: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> 0., py=  0.,
>>  Atom #   3: total charge =   0.0001, s =  0.,
>>  Atom #   3: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> 0., py=  0.,
>>  Atom #   4: total charge =   0., s =  0.,
>>  Atom #   4: total charge =   0., p =  0., pz=  0., px=  
>> 0., py=  0.,
>>  Atom #   5: total charge =   0.0001, s =  0.,
>>  Atom #   5: total charge =   0.0001, p =  0.0001, pz=  0., px=  
>> 0., py=  0.,
>>  Atom #   6: total charge =   0.0001, s =  0.,
>> 
>> 
>> Could you please give me some advice of what I'm doing wrong?
>> 
>> 
>> The projwcf input:
>> 
>>  
>>   prefix = './3cell-cb_scf' ,
>>   outdir = '.' ,
>>   ngauss = 0.1 ,
>>   DeltaE = 0.01 ,
>>  /
>> 
>> 
>> The scf input:
>> 
>>  
>>  calculation = 'scf' ,
>> restart_mode = 'from_scratch' ,
>>   outdir = '.' ,
>>   wfcdir = './tmp' ,
>>   pseudo_dir = '.' ,
>>   prefix = '3cell-cb_scf' ,
>>nstep = 1000 ,
>>  tstress = .false. ,
>>  /
>>  
>>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 = 0.00 ,
>>  /
>>  
>> electron_maxstep = 200 ,
>> scf_must_converge = .false. ,
>> diagonalization='cg' ,
>>  /
>>  
>> 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
>> S1.409356288   3.492127081   4.353797199
>> S1.409009361   3.492914431   7.500696022
>> Mo   2.974783806   4.416004278   5.927352435
>> S2.991861295   6.232688291   4.353114990
>> S2.991733615   6.233889787   7.500216780
>> Mo   4.557309411   7.156655993   5.926482117
>> S4.574550104  8.974187415 4.353268832
>> S4.573865790  8.974308816 7.47172
>> Mo   4.556900653   1.675497042   5.926861427
>> S4.573955171   3.492114510   4.352949498
>> S4.574377417   3.492858021   7.500504130
>> Mo   6.139333906   4.416035304   5.926363713
>> S6.156932316   6.232998289   4.352535948
>> S

Re: [Pw_forum] All Lowdin charges are zero

[Giuseppe Mattioli]

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., s =  0.,
>  Atom #   1: total charge =   0., p =  0., pz=  0., px=  
> 0., py=  0.,
>  Atom #   2: total charge =   0.0001, s =  0.,
>  Atom #   2: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> 0., py=  0.,
>  Atom #   3: total charge =   0.0001, s =  0.,
>  Atom #   3: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> 0., py=  0.,
>  Atom #   4: total charge =   0., s =  0.,
>  Atom #   4: total charge =   0., p =  0., pz=  0., px=  
> 0., py=  0.,
>  Atom #   5: total charge =   0.0001, s =  0.,
>  Atom #   5: total charge =   0.0001, p =  0.0001, pz=  0., px=  
> 0., py=  0.,
>  Atom #   6: total charge =   0.0001, s =  0.,
> 
> 
> Could you please give me some advice of what I'm doing wrong?
> 
> 
> The projwcf input:
> 
>  
>   prefix = './3cell-cb_scf' ,
>   outdir = '.' ,
>   ngauss = 0.1 ,
>   DeltaE = 0.01 ,
>  /
> 
> 
> The scf input:
> 
>  
>  calculation = 'scf' ,
> restart_mode = 'from_scratch' ,
>   outdir = '.' ,
>   wfcdir = './tmp' ,
>   pseudo_dir = '.' ,
>   prefix = '3cell-cb_scf' ,
>nstep = 1000 ,
>  tstress = .false. ,
>  /
>  
>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 = 0.00 ,
>  /
>  
> electron_maxstep = 200 ,
> scf_must_converge = .false. ,
> diagonalization='cg' ,
>  /
>  
> 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
> S1.409356288   3.492127081   4.353797199
> S1.409009361   3.492914431   7.500696022
> Mo   2.974783806   4.416004278   5.927352435
> S2.991861295   6.232688291   4.353114990
> S2.991733615   6.233889787   7.500216780
> Mo   4.557309411   7.156655993   5.926482117
> S4.574550104   8.974187415   4.353268832
> S4.573865790   8.974308816   7.47172
> Mo   4.556900653   1.675497042   5.926861427
> S4.573955171   3.492114510   4.352949498
> S4.574377417   3.492858021   7.500504130
> Mo   6.139333906   4.416035304   5.926363713
> S6.156932316   6.232998289   4.352535948
> S6.156651090   6.233324282   7.500124138
> Mo   7.721896396   7.156797182   5.926687354
> S7.739160210   8.97422   4.353457824
> S7.739048493   8.974459743   7.500654977
> Mo   7.722031044   1.675217921   5.926454615
> S7.739331052   3.492171149   4.352920557
> S7.738377057   3.492639347   7.499947690
> Mo   9.304280720   4.416123626   5.927097215
> S9.321652087   6.232837357   4.353059451
> S9.321594176   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
> C5.700416780   4.960942076  11.705590151
> C5.786661978   6.354516349  11.705273773
> C7.046391983   6.956535202  11.705217371
> C8.203237318   6.173116561  11.705190411
> C8.099168585   4.780492709  11.705023203
> C6.846678887   

[Pw_forum] All Lowdin charges are zero

[Semen Yesylevskyy]

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., s =  0.,
 Atom #   1: total charge =   0., p =  0., pz=  0., px=  
0., py=  0.,
 Atom #   2: total charge =   0.0001, s =  0.,
 Atom #   2: total charge =   0.0001, p =  0.0001, pz=  0., px=  
0., py=  0.,
 Atom #   3: total charge =   0.0001, s =  0.,
 Atom #   3: total charge =   0.0001, p =  0.0001, pz=  0., px=  
0., py=  0.,
 Atom #   4: total charge =   0., s =  0.,
 Atom #   4: total charge =   0., p =  0., pz=  0., px=  
0., py=  0.,
 Atom #   5: total charge =   0.0001, s =  0.,
 Atom #   5: total charge =   0.0001, p =  0.0001, pz=  0., px=  
0., py=  0.,
 Atom #   6: total charge =   0.0001, s =  0.,


Could you please give me some advice of what I'm doing wrong? 


The projwcf input:

 
  prefix = './3cell-cb_scf' ,
  outdir = '.' ,
  ngauss = 0.1 ,
  DeltaE = 0.01 ,
 /


The scf input:

 
 calculation = 'scf' ,
    restart_mode = 'from_scratch' ,
  outdir = '.' ,
  wfcdir = './tmp' ,
  pseudo_dir = '.' ,
  prefix = '3cell-cb_scf' ,
   nstep = 1000 ,
 tstress = .false. ,
 /
 
   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 = 0.00 ,
 /
 
    electron_maxstep = 200 ,
    scf_must_converge = .false. ,
    diagonalization='cg' ,
 /
 
    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   7.47172
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   8.97422   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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