[Pw_forum] U calculation error

Peng Chen pchen at ion.chem.utk.edu
Sun Jul 29 19:00:44 CEST 2012


Dear Dr. Matteo,

I compiled the code with the parameters in make.sys. The n1=n2=n3=1 case is
done without error, but the results for Ni and O are negative which should
not be correct.
26 -14.8678837915617 7.56505581785392 -0.681000339374195
I plot dn.1.da.1.dat and dn0.1.da.1.dat, the data in dn0.1.da.1.dat are not
linear. The scf calculation is converged to 0.001 Ry. So I am not sure what
can cause the problem.

I've attached the Umat_afm.1.out which may contain some useful information
for you. I also put below the input for scf and perturbation on Ni
(alpha=-0.15,-0.07,0.0,0.07,0.15). Same calculations are done for V and O
as well with perturbed V or O atom translated to the origin of the unit
cell.


scf calculation input:

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='nvoprim.afm.ucalc.Ni',
    pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
    outdir='/data/pchen/qe/'
    wf_collect=.TRUE.
 /
 &system
    ibrav=0, celldm(1)=11.19096,
     nat=26, ntyp=6,
  nspin = 2,  starting_magnetization(1)=0.6,
    starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
 starting_magnetization(4)=-0.5,
 ecutwfc = 100, ecutrho = 800,
 occupations ='smearing',
    smearing ='mv',
    degauss = 0.005,nbnd=135
  lda_plus_u = .true.
    Hubbard_U(1)= 1.d-20
    Hubbard_U(2)= 1.d-20
 Hubbard_U(3)= 1.d-20
 Hubbard_U(4)= 1.d-20
 Hubbard_U(5)= 1.d-20
 Hubbard_U(6)= 1.d-20
 /
 &electrons
    conv_thr = 1.0e-7
    mixing_beta = 0.3
 /
CELL_PARAMETERS
0.5 0.96015 0
0.5 -0.96015 0
0 0   1.38889
ATOMIC_SPECIES
 Ni1 58.6934 Ni.pz-n-rrkjus.UPF
 Ni2 58.6934 Ni.pz-n-rrkjus.UPF
 Ni3 58.6934 Ni.pz-n-rrkjus.UPF
 Ni4 58.6934 Ni.pz-n-rrkjus.UPF
 V 50.9415 V.pz-spn-rrkjus.UPF
 O  15.9994  O.pz-n-rrkjus.UPF
ATOMIC_POSITIONS crystal
Ni1      0.000000000   0.000000000   0.000000000
Ni2      0.500000000   0.500000000   0.500000000
Ni3      0.122863290   0.378190177   0.749934361
Ni3      0.877136710   0.621809823   0.250065639
Ni4      0.377137388   0.121809201   0.249932658
Ni4      0.622862612   0.878190799   0.750067342
V        0.373618754   0.623612138   0.115867980
V        0.126381501   0.876388862   0.615868582
V        0.626381246   0.376387862   0.884132020
V        0.873618499   0.123611138   0.384131418
O        0.241839036   0.756304999   0.223613779
O        0.258160617   0.743693910   0.723611944
O        0.758160964   0.243695001   0.776386221
O        0.741839383   0.256306090   0.276388056
O       -0.000998332   1.000227439   0.243205274
O        0.500997862   0.499772508   0.743208489
O        1.000998332  -0.000227439   0.756794726
O        0.499002138   0.500227492   0.256791511
O        0.381099639   0.150692971   0.006796703
O        0.118898786   0.349304325   0.506798051
O        0.149581603   0.378555571   0.991989919
O        0.350419534   0.121445697   0.491991443
O        0.618900361   0.849307029   0.993205297
O        0.881101214   0.650695675   0.493203949
O        0.850418397   0.621444429   0.008012081
O        0.649580466   0.878554303   0.508010557

K_POINTS (automatic)
 5 5 5 1 1 1

Perturbation on Ni with alpha=0.15 input:

&control
    calculation='scf'
    restart_mode='from_scratch',
    prefix='nvoprim.afm.ucalc.Ni',
    pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',
    outdir='/data/pchen/qe/'
   wf_collect=.TRUE.
 /
 &system
    ibrav=0, celldm(1)=11.19096,
     nat=26, ntyp=6,
  nspin = 2,  starting_magnetization(1)=0.6,
    starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,
 starting_magnetization(4)=-0.5,
 ecutwfc = 100, ecutrho = 800,
 occupations ='smearing',
    smearing ='mv',
    degauss = 0.005,nbnd=135
  lda_plus_u = .true.
    Hubbard_U(1)= 1.d-20
    Hubbard_U(2)= 1.d-20
    Hubbard_U(3)= 1.d-20
Hubbard_U(4)= 1.d-20
Hubbard_U(5)= 1.d-20
Hubbard_U(6)= 1.d-20

    Hubbard_alpha(1)= 0.15
 /
 &electrons
    conv_thr = 1.0e-7
    mixing_beta = 0.3
  startingpot='file'
 startingwfc='file'
 diago_thr_init=5.09E-11,
 /
CELL_PARAMETERS
0.5 0.96015 0
0.5 -0.96015 0
0 0   1.38889
ATOMIC_SPECIES
 Ni1 58.6934 Ni.pz-n-rrkjus.UPF
 Ni2 58.6934 Ni.pz-n-rrkjus.UPF
 Ni3 58.6934 Ni.pz-n-rrkjus.UPF
 Ni4 58.6934 Ni.pz-n-rrkjus.UPF
 V 50.9415 V.pz-spn-rrkjus.UPF
 O  15.9994  O.pz-n-rrkjus.UPF
ATOMIC_POSITIONS crystal
Ni1      0.000000000   0.000000000   0.000000000
Ni2      0.500000000   0.500000000   0.500000000
Ni3      0.122863290   0.378190177   0.749934361
Ni3      0.877136710   0.621809823   0.250065639
Ni4      0.377137388   0.121809201   0.249932658
Ni4      0.622862612   0.878190799   0.750067342
V        0.373618754   0.623612138   0.115867980
V        0.126381501   0.876388862   0.615868582
V        0.626381246   0.376387862   0.884132020
V        0.873618499   0.123611138   0.384131418
O        0.241839036   0.756304999   0.223613779
O        0.258160617   0.743693910   0.723611944
O        0.758160964   0.243695001   0.776386221
O        0.741839383   0.256306090   0.276388056
O       -0.000998332   1.000227439   0.243205274
O        0.500997862   0.499772508   0.743208489
O        1.000998332  -0.000227439   0.756794726
O        0.499002138   0.500227492   0.256791511
O        0.381099639   0.150692971   0.006796703
O        0.118898786   0.349304325   0.506798051
O        0.149581603   0.378555571   0.991989919
O        0.350419534   0.121445697   0.491991443
O        0.618900361   0.849307029   0.993205297
O        0.881101214   0.650695675   0.493203949
O        0.850418397   0.621444429   0.008012081
O        0.649580466   0.878554303   0.508010557

K_POINTS (automatic)
 5 5 5 1 1 1



On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <matteo at umn.edu> wrote:

> Dear Peng,
>
> I'm not very expert of compiling codes. You have to make sure that all
> the libraries are linked correctly for the code to work. I assume you
> have QE installed on the same computer. You could give a look in the
> make.sys to check what is the correct way to link them. If everything
> is consistent, then you have to find out where the code is failing.
> have you tried to run with n1 = n2 = n3 = 1? what did you get?
>
> Matteo
>
>
>
> On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> > Dear Dr. Matteo,
> >
> > I used command listed below to compile resp_mat.f90. No error in
> compiling.
> > I am not sure if I did right in choosing the libs.
> > ifort  -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"
> > -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3  -lmkl_sequential
> -lmkl_core
> >
> > The libs in mkl are shown below:
> > libmkl_avx.so                   libmkl_intel_sp2dp.so
> > libmkl_blacs_ilp64.a            libmkl_intel_thread.a
> > libmkl_blacs_intelmpi_ilp64.a   libmkl_intel_thread.so
> > libmkl_blacs_intelmpi_ilp64.so  libmkl_lapack95_ilp64.a
> > libmkl_blacs_intelmpi_lp64.a    libmkl_lapack95_lp64.a
> > libmkl_blacs_intelmpi_lp64.so   libmkl_lapack.so
> > libmkl_blacs_lp64.a             libmkl_mc3.so
> > libmkl_blacs_openmpi_ilp64.a    libmkl_mc.so
> > libmkl_blacs_openmpi_lp64.a     libmkl_p4n.so
> > libmkl_blacs_sgimpt_ilp64.a     libmkl_pgi_thread.a
> > libmkl_blacs_sgimpt_lp64.a      libmkl_pgi_thread.so
> > libmkl_blas95_ilp64.a           libmkl_scalapack_ilp64.a
> > libmkl_blas95_lp64.a            libmkl_scalapack_ilp64.so
> > libmkl_cdft_core.a              libmkl_scalapack_lp64.a
> > libmkl_core.a                   libmkl_scalapack_lp64.so
> > libmkl_core.so                  libmkl_sequential.a
> > libmkl_def.so                   libmkl_sequential.so
> > libmkl_gf_ilp64.a               libmkl_solver_ilp64.a
> > libmkl_gf_ilp64.so              libmkl_solver_ilp64_sequential.a
> > libmkl_gf_lp64.a                libmkl_solver_lp64.a
> > libmkl_gf_lp64.so               libmkl_solver_lp64_sequential.a
> > libmkl_gnu_thread.a             libmkl_vml_avx.so
> > libmkl_gnu_thread.so            libmkl_vml_def.so
> > libmkl_intel_ilp64.a            libmkl_vml_mc2.so
> > libmkl_intel_ilp64.so           libmkl_vml_mc3.so
> > libmkl_intel_lp64.a             libmkl_vml_mc.so
> > libmkl_intel_lp64.so            libmkl_vml_p4n.so
> > libmkl_intel_sp2dp.a            locale
> >
> >
> > Some errors in output:
> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > Image              PC                Routine            Line
>  Source
> > r.x                0000000000445659  Unknown               Unknown
>  Unknown
> > r.x                000000000040A363  Unknown               Unknown
>  Unknown
> > r.x                000000000040338C  Unknown               Unknown
>  Unknown
> > libc.so.6          00002B85B9495994  Unknown               Unknown
>  Unknown
> > r.x                0000000000403289  Unknown               Unknown
>  Unknown
> >
> >
> > On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <matteo at umn.edu>
> wrote:
> >>
> >> Dear Peng,
> >>
> >> nothing looks wrong in your input. have you tried with n1, n2, n3 all
> >> equal to 1? are you sure you compiled correctly?
> >>
> >> Matteo
> >>
> >>
> >>
> >> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> wrote:
> >> > Dear Dr. Matteo,
> >> >
> >> > The primitive cell has 26 atoms with 3 different types. The pos and
> >> > resp_mat.in files are shown below:
> >> >
> >> > 5.6087 10.79 0.0
> >> > 5.6087 -10.79 0.0
> >> > 0.0 0.0   15.570873
> >> > 0       0       0       1
> >> > 0.5     0.5     0.5     -1
> >> > 0.12286329      0.378190177     0.749934361     1
> >> > 0.87713671      0.621809823     0.250065639     1
> >> > 0.377137388     0.121809201     0.249932658     -1
> >> > 0.622862612     0.878190799     0.750067342     -1
> >> > 0.373618754     0.623612138     0.11586798      0
> >> > 0.126381501     0.876388862     0.615868582     0
> >> > 0.626381246     0.376387862     0.88413202      0
> >> > 0.873618499     0.123611138     0.384131418     0
> >> > 0.241839036     0.756304999     0.223613779     0
> >> > 0.258160617     0.74369391      0.723611944     0
> >> > 0.758160964     0.243695001     0.776386221     0
> >> > 0.741839383     0.25630609      0.276388056     0
> >> > -0.000998332    1.000227439     0.243205274     0
> >> > 0.500997862     0.499772508     0.743208489     0
> >> > 1.000998332     -0.000227439    0.756794726     0
> >> > 0.499002138     0.500227492     0.256791511     0
> >> > 0.381099639     0.150692971     0.006796703     0
> >> > 0.118898786     0.349304325     0.506798051     0
> >> > 0.149581603     0.378555571     0.991989919     0
> >> > 0.350419534     0.121445697     0.491991443     0
> >> > 0.618900361     0.849307029     0.993205297     0
> >> > 0.881101214     0.650695675     0.493203949     0
> >> > 0.850418397     0.621444429     0.008012081     0
> >> > 0.649580466     0.878554303     0.508010557     0
> >> >
> >> > resp_mat.in :
> >> >  &input_mat
> >> >    ntyp = 3
> >> >    na(1) = 6
> >> >    na(2) = 4
> >> >    na(3) = 16
> >> >    nalfa = 5
> >> >    magn=.true.
> >> >    filepos = 'pos'
> >> >    back = 'no'
> >> >    filednda = 'file_afm'
> >> >    n1 = 2
> >> >    n2 = 2
> >> >    n3 = 2
> >> >  &end
> >> >
> >> >
> >> >
> >> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <matteo at umn.edu>
> >> > wrote:
> >> >>
> >> >> Dear Peng,
> >> >>
> >> >> can you provide info about your system? maybe it is larger than the
> >> >> maximum size allowed by r.x?
> >> >>
> >> >> Matteo
> >> >>
> >> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <pchen at ion.chem.utk.edu>
> >> >> wrote:
> >> >> > Dear All,
> >> >> >
> >> >> > There are some errors when I run r.x to calculate the U. I used
> >> >> > Espresso-5.0
> >> >> > and follow the steps in LSDA+U example. I am not sure what could be
> >> >> > wrong.
> >> >> > And if you need other input/output, please let me know.
> >> >> >
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> >> > r.x                081DDFDA  Unknown               Unknown  Unknown
> >> >> > r.x                081FA33B  Unknown               Unknown  Unknown
> >> >> > r.x                081F9C5C  Unknown               Unknown  Unknown
> >> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (8): internal consistency check failure, file
> >> >> > ./src/libfor/for_wseq_lis.c, line 635
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0822DACC  Unknown               Unknown  Unknown
> >> >> > r.x                0822C265  Unknown               Unknown  Unknown
> >> >> > r.x                082071FA  Unknown               Unknown  Unknown
> >> >> > r.x                081DD664  Unknown               Unknown  Unknown
> >> >> > r.x                081F9AF7  Unknown               Unknown  Unknown
> >> >> > r.x                0804E38F  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                0804DAED  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> >> > Image              PC        Routine            Line        Source
> >> >> > r.x                08253657  Unknown               Unknown  Unknown
> >> >> > r.x                081F4087  Unknown               Unknown  Unknown
> >> >> > r.x                081DCDB7  Unknown               Unknown  Unknown
> >> >> > r.x                081DF354  Unknown               Unknown  Unknown
> >> >> > r.x                081DD672  Unknown               Unknown  Unknown
> >> >> > r.x                081DF5E8  Unknown               Unknown  Unknown
> >> >> > Unknown            FFFFE600  Unknown               Unknown  Unknown
> >> >> > r.x                0804824A  Unknown               Unknown  Unknown
> >> >> > r.x                0823805D  Unknown               Unknown  Unknown
> >> >> > r.x                08048131  Unknown               Unknown  Unknown
> >> >> >
> >> >> >
> >> >> > --
> >> >> >   Best Regards.
> >> >> >         Peng
> >> >> >
> >> >> > _______________________________________________
> >> >> > Pw_forum mailing list
> >> >> > Pw_forum at pwscf.org
> >> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Matteo Cococcioni
> >> >> Department of Chemical Engineering and Materials Science,
> >> >> University of Minnesota
> >> >> 421 Washington Av. SE
> >> >> Minneapolis, MN 55455
> >> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> >> _______________________________________________
> >> >> Pw_forum mailing list
> >> >> Pw_forum at pwscf.org
> >> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> >   Best Regards.
> >> >         Peng
> >> >
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > Pw_forum at pwscf.org
> >> > http://www.democritos.it/mailman/listinfo/pw_forum
> >> >
> >>
> >>
> >>
> >> --
> >> Matteo Cococcioni
> >> Department of Chemical Engineering and Materials Science,
> >> University of Minnesota
> >> 421 Washington Av. SE
> >> Minneapolis, MN 55455
> >> Tel. +1 612 624 9056    Fax +1 612 626 7246
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> >
> >
> > --
> >   Best Regards.
> >         Peng
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Matteo Cococcioni
> Department of Chemical Engineering and Materials Science,
> University of Minnesota
> 421 Washington Av. SE
> Minneapolis, MN 55455
> Tel. +1 612 624 9056    Fax +1 612 626 7246
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
  Best Regards.
        Peng
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