[Pw_forum] U calculation error

Matteo Cococcioni matteo at umn.edu
Sun Jul 29 19:17:59 CEST 2012


Dear Peng,

I advise you to run the example available from the QE webpage and try
to reproduce the same results.

On Sun, Jul 29, 2012 at 12:00 PM, Peng Chen <pchen at ion.chem.utk.edu> wrote:
> 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.


ok then maybe you can try to increase them one per time and see at
what level the code stops with error?


> 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.


this is not related to the error message of r.x but is not right. if
you want reliable results you have to get these plots linear.



The scf calculation is converged to 0.001 Ry. So I am not sure what
> can cause the problem.


yes probably this is not enough. the inputs look fine (I haven't
looked inside the response matrix) but you have to make sure the scf
potential and wfc are saved after the unperturbed scf run and every
perturbed calculation starts from them.
do you really need 100 Ry cut off with US PP?

Matteo


>
> 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
>
> _______________________________________________
> 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



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