[Wien] Charge leakage too large
Chithra M Mathew
chithramm at nirmalagiricollege.ac.in
Fri Jun 14 08:42:08 CEST 2024
Hi Gavin Abo
The output I'm receiving doesn't match what I expected when using the
provided .struct file. Could you assist me in understanding why the
output differs or help me troubleshoot the issue?
SELECT XCPOT:
recommended: PBE [(13) GGA of Perdew-Burke-Ernzerhof 96]
LDA [( 5)]
WC [(11) GGA of Wu-Cohen 2006]
PBESOL [(19) GGA of Perdew etal. 2008]
SELECT ENERGY to separate core and valence states:
recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
ALTERNATIVELY: specify charge localization
(between 0.97 and 1.0) to select core state
Atomic configuration for atom: Zn Z= 30.00
E-up(Ry) E-dn(Ry) Occupancy q/sphere core-state
1S -699.940288 -699.940288 1.00 1.00 1.0000 T
2S -85.104763 -85.104763 1.00 1.00 1.0000 T
2P* -74.944685 -74.944685 1.00 1.00 1.0000 T
2P -73.190086 -73.190086 2.00 2.00 1.0000 T
3S -9.495639 -9.495639 1.00 1.00 0.9995 T
3P* -6.279899 -6.279899 1.00 1.00 0.9984 T
3P -6.054663 -6.054663 2.00 2.00 0.9982 T
3D* -0.761030 -0.761030 2.00 2.00 0.9526 F
3D -0.734827 -0.734827 3.00 3.00 0.9504 F
4S -0.439409 -0.439409 1.00 1.00 0.2953 F
:WARNING: 0.011 Zn CORE electrons leak out of MT-sphere !!!!
:WARNING: touch .lcore and run scf-cycle with core density superposition
:WARNING: Or: rerun lstart with lower E-core separation energy
:WARNING: ORBITAL: 3S -9.496 -9.496
:WARNING: ORBITAL: 3P* -6.280 -6.280
:WARNING: ORBITAL: 3P -6.055 -6.055
Atomic configuration for atom: O Z= 8.00
E-up(Ry) E-dn(Ry) Occupancy q/sphere core-state
1S -37.835755 -37.745366 1.00 1.00 1.0000 T
2S -1.852847 -1.614226 1.00 1.00 0.8687 F
2P* -0.752776 -0.529460 1.00 1.00 0.7794 F
2P -0.749999 -0.526947 2.00 0.00 0.8020 F
LSTART ENDS
WARNING: 0.011 Zn CORE electrons leak out of MT-sphere !!!!
file .lcore created, scf-cycle with core-density superposition !
> inputfiles prepared (12:07:42)
inputfiles prepared
inversion is NOT present
> inputfiles for lapw1c/2c prepared, no inversion present (12:07:42)
next is kgen
12 symmetry operations without inversion
inversion added (non-spinpolarized non-so calculation)
NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
length of reciprocal lattice vectors: 1.185 1.185 0.637 12.299
12.299 6.611
76 k-points generated, ndiv= 12 12 6
KGEN ENDS
next is dstart
> dstart -c -p > & .mist (12:07:42) running dstart in single mode
C T F
DSTART ENDS
0.788u 0.008s 0:00.21 371.4% 0+0k 0+1016io 0pf+0w
-----> new Z.in0 generated
init_lapw finished ok
On Fri, 14 Jun 2024 at 10:32, Gavin Abo <gabo13279 at gmail.com> wrote:
>
> Does attached struct file give same NEC error for you? It has some
> differences. For example, it doesn't have the special labels such as
> "Zn1" like in your struct.
>
> ZnO structure parameters were used from
>
> https://next-gen.materialsproject.org/materials/mp-2133#summary
>
> They were put in StructGen, after clicking "set automatically RM and
> continue editing" the Reduce RMTs by 0% using new scheme was used for
> creating the ZnO.struct file.
>
> Below is what happened on my system:
>
> username at computername:~/wiendata/ZnO$ lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: Ubuntu 24.04 LTS
> Release: 24.04
> Codename: noble
> username at computername:~/wiendata/ZnO$ cat $WIENROOT/WIEN2k_VERSION
> WIEN2k_23.2 (Release 9/3/2022)
> username at computername:~/wiendata/ZnO$ ls -l
> total 4
> -rw-rw-r-- 1 username username 954 Jun 13 22:44 ZnO.struct
> username at computername:~/wiendata/ZnO$ init_lapw -b
> next is setrmt
> next is nn
> specify nn-bondlength factor: (usually=2) [and optionally dlimit,
> dstmax (about 1.d-5, 20)]
> dfac,DSTMAX: 2.0000000000000000 20.000000000000000
> iix,iiy,iiz 4 4 3
> 24.490860000000001 24.490860000000001 29.593122000000001
>
> ATOM 1 Zn ATOM 2 O
> RMT( 1)=1.99000 AND RMT( 2)=1.72000
> SUMS TO 3.71000 LT. NN-DIST= 3.73063
>
> ATOM 2 O ATOM 1 Zn
> RMT( 2)=1.72000 AND RMT( 1)=1.99000
> SUMS TO 3.71000 LT. NN-DIST= 3.73063
> STOP NN ENDS
> 0.003u 0.000s 0:00.00 0.0% 0+0k 0+56io 0pf+0w
> next is sgroup
> > sgroup (22:46:00) 0.000u 0.000s 0:00.00 0.0% 0+0k 0+8io 0pf+0w
> Names of point group: 3m1 3m1 C3v
> Names of point group: 3m1 3m1 C3v
> Number and name of space group: 186 (P 63 m c)
> next is symmetry
> > symmetry (22:46:00) SPACE GROUP DOES NOT CONTAIN INVERSION
> 0.000u 0.000s 0:00.00 0.0% 0+0k 192+40io 1pf+0w
> next is lstart
> 2 Atoms found: with labels Zn O
> generate atomic configuration for atom 1 : Zn
> generate atomic configuration for atom 2 : O
> SELECT XCPOT:
> recommended: PBE [(13) GGA of Perdew-Burke-Ernzerhof 96]
> LDA [( 5)]
> WC [(11) GGA of Wu-Cohen 2006]
> PBESOL [(19) GGA of Perdew etal. 2008]
> SELECT ENERGY to separate core and valence states:
> recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere)
> ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to
> select core state
> STOP LSTART ENDS
> file .lcore created, scf-cycle with core-density superposition !
> 1.7200 8
> set RKmax = 6.25333333333333333333
> set LVNS = 6
> set GMAX = 16.0
> set IFFTfac = 2.0
> > inputfiles prepared (22:46:00)
> inputfiles prepared
> inversion is NOT present
> > inputfiles for lapw1c/2c prepared, no inversion present (22:46:00)
> next is kgen
> STOP KGEN ENDS
> NUMK: 1000
> basic k-mesh: 12, 12, 7 = 1008, kfactor = 1
> 12 symmetry operations without inversion
> inversion added (non-spinpolarized non-so calculation)
> NUMBER OF K-POINTS IN WHOLE CELL: (0 for 3 divisions of K, -1 for
> delta-K)
> length of reciprocal lattice vectors (bohr^-1): 1.185 1.185 0.637
> 76 k-points generated, ndiv= 12 12 6
> delta-K (bohr^-1): 0.0987 0.0987 0.1062
> STOP KGEN ENDS
> next is dstart
> > dstart -c -p > & .mist (22:46:00) running dstart in single mode
> STOP DSTART ENDS
> 0.528u 0.007s 0:00.54 96.2% 0+0k 4096+1288io 13pf+0w
>
> -----> new ZnO.in0 generated
> init_lapw finished ok
> username at computername:~/wiendata/ZnO$ run_lapw
> STOP LAPW0 END
> STOP LAPW1 END
> STOP LAPW2 END
> STOP CORE END
> STOP DSTART ENDS
> STOP MIXER END
> ec cc fc and str_conv 0 1 1 1
> in cycle 2 ETEST: 0 CTEST: 0 STRTEST: 0
> STOP LAPW0 END
> STOP LAPW1 END
> STOP LAPW2 END
> STOP CORE END
> STOP DSTART ENDS
> STOP MIXER END
> ec cc fc and str_conv 0 1 1 1
> ...
> in cycle 7 ETEST: .0024352750000000 CTEST: .0096356 STRTEST: 0
> STOP LAPW0 END
> STOP LAPW1 END
> STOP LAPW2 END
> STOP CORE END
> STOP DSTART ENDS
> STOP MIXER END
> ec cc fc and str_conv 0 1 1 1
> in cycle 8 ETEST: .0006986500000000 CTEST: .0065417 STRTEST: 0
> STOP LAPW0 END
> STOP LAPW1 END
> STOP LAPW2 END
> STOP CORE END
> STOP DSTART ENDS
> STOP MIXER END
> ec cc fc and str_conv 1 1 1 1
>
> > stop
>
> On 6/13/2024 10:32 PM, Chithra M Mathew wrote:
> > @Fecher, Gerhard
> >
> > On Tue, 11 Jun 2024 at 20:13, Fecher, Gerhard <fecher at uni-mainz.de> wrote:
> >> you have never shown your case.struct file !!!
> >>
> >> your NEC01: is realy strange
> >>
> >> I was recently running ZnO with wurtzide structure and had no problems.
> >>
> >> Ciao
> >> Gerhard
> >>
> >> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> >> "I think the problem, to be quite honest with you,
> >> is that you have never actually known what the question is."
> >>
> >> ====================================
> >> Dr. Gerhard H. Fecher
> >> Institut of Physics
> >> Johannes Gutenberg - University
> >> 55099 Mainz
> >> ________________________________________
> >> Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von Chithra M Mathew [chithramm at nirmalagiricollege.ac.in]
> >> Gesendet: Dienstag, 11. Juni 2024 12:37
> >> An: A Mailing list for WIEN2k users
> >> Betreff: Re: [Wien] Charge leakage too large
> >>
> >> Thank you for the response
> >> I tried RMT value for Zn 2.1 and for O from 1.62 to 1.4.
> >> Initialisation is done without error.
> >>
> >> .scfm file
> >> NEC01: NUCLEAR AND ELECTRONIC CHARGE 76.00000 70.29675
> >> :WAR : NEC01: average large charge leakage: 1.42581229073737 e/atom
> >> :ERROR : NEC01: average charge leakage too large: 1.42581229073737 e/atom
> >> Check FERMI method (use TEMP(S) for 2D), check symmetry (rounding
> >> errors in case.struct)
> >>
> >> output file
> >> :WARNING: Iteration 1 occurs more than once in this scf file!!!
> >>
> >> Dont know how to rectify this.
> >> ZnO.lcore file is empty
> >>
> >> On Tue, 11 Jun 2024 at 13:34, Peter Blaha <peter.blaha at tuwien.ac.at> wrote:
> >>> Hi,
> >>>
> >>> Please use the RMTs (or stay close to them) which setrmt recommends.
> >>> Your O sphere is very small and unless there is a particular reason (eg.
> >>> total energies for the O2 molecule is necessary, ....) I would not do that.
> >>>
> >>> For small Zn spheres, reducing the ecut to -7 is the proper way to do.
> >>>
> >>> Your core leakage error must come from somewhere else.
> >>>
> >>> Please check your case.scfm file (:NEC01 and core charges) and also
> >>> case.outputm.
> >>> You should find out what causes the large charge leakage. Maybe case.in2
> >>> (NE) is wrong, ....
> >>>
> >>>
> >>> Am 11.06.2024 um 09:14 schrieb Chithra M Mathew:
> >>>> Sorry I'm new to Wien2k.
> >>>> The lattice parameters are ok and the positions given in the correct
> >>>> coordinates.
> >>>> In setting up the calculation the default RMT's mean that there is
> >>>> core charge leakage. Then RMT value for Zn 2.1 and for O 1.4 used.
> >>>> Tried the separation to -7.0Ry (Zn 3P core level binding energy 6.69Ry)
> >>>> I also attempted to reduce RKmax to adjust for the smaller value of
> >>>> RMTmin, but the same type of error occurs.
> >>>> Initialisation is done without error.
> >>>> But when do scf cycle
> >>>>
> >>>> LAPW0 END
> >>>> LAPW1 END
> >>>> LAPW2 END
> >>>> CORE END
> >>>> ERROR: NEC01 charge leakage too large
> >>>>
> >>>> Is there something else that I should be doing in the setup?
> >>>>
> >>>> On Mon, 10 Jun 2024 at 15:50, Fecher, Gerhard <fecher at uni-mainz.de> wrote:
> >>>>> Like usual:
> >>>>> Check you’re structure, are the lattice parameters ok and the positions given in the correct coordinates ?
> >>>>> Change the RMTs, where are they coming from ?
> >>>>> Decrease energy to separate core and valence, which value did you use ? are the Zn 3p in the core ?
> >>>>> Search the mailing list to find what others did when they hit this problem
> >>>>>
> >>>>> Ciao
> >>>>> Gerhard
> >>>>>
> >>>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> >>>>> "I think the problem, to be quite honest with you,
> >>>>> is that you have never actually known what the question is."
> >>>>>
> >>>>> ====================================
> >>>>> Dr. Gerhard H. Fecher
> >>>>> Institut of Physics
> >>>>> Johannes Gutenberg - University
> >>>>> 55099 Mainz
> >>>>> ________________________________________
> >>>>> Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von Chithra M Mathew [chithramm at nirmalagiricollege.ac.in]
> >>>>> Gesendet: Montag, 10. Juni 2024 10:42
> >>>>> An: A Mailing list for WIEN2k users
> >>>>> Betreff: [Wien] Charge leakage too large
> >>>>>
> >>>>> Hi
> >>>>> When conducting the SCF cycle for ZnO, I'm facing a charge leakage error. How to solve this.
> >>>>>
> >>>>>
> >>>>> LAPW0 END
> >>>>> LAPW1 END
> >>>>> LAPW2 END
> >>>>> CORE END
> >>>>> ERROR: NEC01 charge leakage too large
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> ATOM 1 Zn ATOM 2 O
> >>>>> RMT( 1)=2.20000 AND RMT( 2)=1.20000
> >>>>> SUMS TO 3.40000 LT. NN-DIST= 3.72997
> >>>>>
> >>>>> ATOM 2 O ATOM 1 Zn
> >>>>> RMT( 2)=1.20000 AND RMT( 1)=2.20000
> >>>>> SUMS TO 3.40000 LT. NN-DIST= 3.72997
> >>>>> NN ENDS
> >>>>>> inputfiles for lapw1c/2c prepared, no inversion present (14:04:46)
> >>>>> next is kgen
> >>>>> 12 symmetry operations without inversion
> >>>>> inversion added (non-spinpolarized non-so calculation)
> >>>>> NUMBER OF K-POINTS IN WHOLE CELL: (0 allows to specify 3 divisions of G)
> >>>>> length of reciprocal lattice vectors: 1.182 1.182 0.639 12.274 12.274 6.638
> >>>>> 76 k-points generated, ndiv= 12 12 6
> >>>>> KGEN ENDS
> >>>>> next is dstart
> >>>>>> dstart -c -p > & .mist (14:04:46) running dstart in single mode
> >>>>> C T F
> >>>>> DSTART ENDS
> >>>>> 0.747u 0.014s 0:00.26 288.4% 0+0k 0+1296io 0pf+0w
> >>>>>
> >>>>> -----> new ZnO.in0 generated
> >>>>> init_lapw finished ok
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Wien mailing list
> >>>>> Wien at zeus.theochem.tuwien.ac.at
> >>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >>>>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> >>>> _______________________________________________
> >>>> Wien mailing list
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> >>>> SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
> >>> --
> >>> --------------------------------------------------------------------------
> >>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> >>> Phone: +43-1-58801-165300
> >>> Email: peter.blaha at tuwien.ac.at WIEN2k: http://www.wien2k.at
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> >>> -------------------------------------------------------------------------
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