[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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