Dear Dr. Matteo,<div><br></div><div>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.</div><div>26 -14.8678837915617 7.56505581785392 -0.681000339374195</div>
<div>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.</div><div><br></div><div>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.</div>
<div>
</div><div><br></div><div>scf calculation input:</div><div><br></div><div>&control</div><div><div> calculation='scf'</div><div> restart_mode='from_scratch',</div><div> prefix='<a href="http://nvoprim.afm.ucalc.Ni" target="_blank">nvoprim.afm.ucalc.Ni</a>',</div>
<div> pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',</div><div> outdir='/data/pchen/qe/'</div><div> wf_collect=.TRUE.</div><div> /</div><div> &system</div><div> ibrav=0, celldm(1)=11.19096,</div>
<div> nat=26, ntyp=6,</div><div> nspin = 2, starting_magnetization(1)=0.6,</div><div> starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,</div><div> starting_magnetization(4)=-0.5,</div><div> ecutwfc = 100, ecutrho = 800,</div>
<div> occupations ='smearing',</div><div> smearing ='mv',</div><div> degauss = 0.005,nbnd=135</div><div> lda_plus_u = .true.</div><div> Hubbard_U(1)= 1.d-20</div><div> Hubbard_U(2)= 1.d-20</div>
<div> Hubbard_U(3)= 1.d-20</div><div> Hubbard_U(4)= 1.d-20</div><div> Hubbard_U(5)= 1.d-20</div><div> Hubbard_U(6)= 1.d-20</div><div> /</div><div> &electrons</div><div> conv_thr = 1.0e-7</div><div> mixing_beta = 0.3</div>
<div> /</div><div>CELL_PARAMETERS</div><div>0.5 0.96015 0</div><div>0.5 -0.96015 0</div><div>0 0 1.38889</div><div><div>ATOMIC_SPECIES</div><div> Ni1 58.6934 Ni.pz-n-rrkjus.UPF</div><div> Ni2 58.6934 Ni.pz-n-rrkjus.UPF</div>
<div> Ni3 58.6934 Ni.pz-n-rrkjus.UPF</div><div> Ni4 58.6934 Ni.pz-n-rrkjus.UPF</div><div> V 50.9415 V.pz-spn-rrkjus.UPF</div><div> O 15.9994 O.pz-n-rrkjus.UPF</div><div>ATOMIC_POSITIONS crystal</div><div>Ni1 0.000000000 0.000000000 0.000000000</div>
<div>Ni2 0.500000000 0.500000000 0.500000000</div><div>Ni3 0.122863290 0.378190177 0.749934361</div><div>Ni3 0.877136710 0.621809823 0.250065639</div><div>Ni4 0.377137388 0.121809201 0.249932658</div>
<div>Ni4 0.622862612 0.878190799 0.750067342</div><div>V 0.373618754 0.623612138 0.115867980</div><div>V 0.126381501 0.876388862 0.615868582</div><div>V 0.626381246 0.376387862 0.884132020</div>
<div>V 0.873618499 0.123611138 0.384131418</div><div>O 0.241839036 0.756304999 0.223613779</div><div>O 0.258160617 0.743693910 0.723611944</div><div>O 0.758160964 0.243695001 0.776386221</div>
<div>O 0.741839383 0.256306090 0.276388056</div><div>O -0.000998332 1.000227439 0.243205274</div><div>O 0.500997862 0.499772508 0.743208489</div><div>O 1.000998332 -0.000227439 0.756794726</div>
<div>O 0.499002138 0.500227492 0.256791511</div><div>O 0.381099639 0.150692971 0.006796703</div><div>O 0.118898786 0.349304325 0.506798051</div><div>O 0.149581603 0.378555571 0.991989919</div>
<div>O 0.350419534 0.121445697 0.491991443</div><div>O 0.618900361 0.849307029 0.993205297</div><div>O 0.881101214 0.650695675 0.493203949</div><div>O 0.850418397 0.621444429 0.008012081</div>
<div>O 0.649580466 0.878554303 0.508010557</div><div><br></div><div>K_POINTS (automatic)</div><div> 5 5 5 1 1 1</div></div><div><br></div><div>Perturbation on Ni with alpha=0.15 input:</div><div><br></div><div>
<div>&control</div><div> calculation='scf'</div><div> restart_mode='from_scratch',</div><div> prefix='<a href="http://nvoprim.afm.ucalc.Ni" target="_blank">nvoprim.afm.ucalc.Ni</a>',</div>
<div> pseudo_dir = '/home/pchen/espresso-5.0/pseudo/',</div>
<div> outdir='/data/pchen/qe/'</div><div> wf_collect=.TRUE.</div><div> /</div><div> &system</div><div> ibrav=0, celldm(1)=11.19096,</div><div> nat=26, ntyp=6,</div><div> nspin = 2, starting_magnetization(1)=0.6,</div>
<div> starting_magnetization(2)=-0.6, starting_magnetization(3)=0.5,</div><div> starting_magnetization(4)=-0.5,</div><div> ecutwfc = 100, ecutrho = 800,</div><div> occupations ='smearing',</div><div> smearing ='mv',</div>
<div> degauss = 0.005,nbnd=135</div><div> lda_plus_u = .true.</div><div> Hubbard_U(1)= 1.d-20</div><div> Hubbard_U(2)= 1.d-20</div><div> Hubbard_U(3)= 1.d-20</div><div>Hubbard_U(4)= 1.d-20</div><div>Hubbard_U(5)= 1.d-20</div>
<div>Hubbard_U(6)= 1.d-20</div><div><br></div><div> Hubbard_alpha(1)= 0.15</div><div> /</div><div> &electrons</div><div> conv_thr = 1.0e-7</div><div> mixing_beta = 0.3</div><div> startingpot='file'</div>
<div> startingwfc='file'</div><div> diago_thr_init=5.09E-11,</div><div> /</div><div>CELL_PARAMETERS</div><div>0.5 0.96015 0</div><div>0.5 -0.96015 0</div><div>0 0 1.38889</div></div><div><div>ATOMIC_SPECIES</div>
<div> Ni1 58.6934 Ni.pz-n-rrkjus.UPF</div><div> Ni2 58.6934 Ni.pz-n-rrkjus.UPF</div><div> Ni3 58.6934 Ni.pz-n-rrkjus.UPF</div><div> Ni4 58.6934 Ni.pz-n-rrkjus.UPF</div><div> V 50.9415 V.pz-spn-rrkjus.UPF</div><div> O 15.9994 O.pz-n-rrkjus.UPF</div>
<div>ATOMIC_POSITIONS crystal</div><div>Ni1 0.000000000 0.000000000 0.000000000</div><div>Ni2 0.500000000 0.500000000 0.500000000</div><div>Ni3 0.122863290 0.378190177 0.749934361</div><div>Ni3 0.877136710 0.621809823 0.250065639</div>
<div>Ni4 0.377137388 0.121809201 0.249932658</div><div>Ni4 0.622862612 0.878190799 0.750067342</div><div>V 0.373618754 0.623612138 0.115867980</div><div>V 0.126381501 0.876388862 0.615868582</div>
<div>V 0.626381246 0.376387862 0.884132020</div><div>V 0.873618499 0.123611138 0.384131418</div><div>O 0.241839036 0.756304999 0.223613779</div><div>O 0.258160617 0.743693910 0.723611944</div>
<div>O 0.758160964 0.243695001 0.776386221</div><div>O 0.741839383 0.256306090 0.276388056</div><div>O -0.000998332 1.000227439 0.243205274</div><div>O 0.500997862 0.499772508 0.743208489</div>
<div>O 1.000998332 -0.000227439 0.756794726</div><div>O 0.499002138 0.500227492 0.256791511</div><div>O 0.381099639 0.150692971 0.006796703</div><div>O 0.118898786 0.349304325 0.506798051</div>
<div>O 0.149581603 0.378555571 0.991989919</div><div>O 0.350419534 0.121445697 0.491991443</div><div>O 0.618900361 0.849307029 0.993205297</div><div>O 0.881101214 0.650695675 0.493203949</div>
<div>O 0.850418397 0.621444429 0.008012081</div><div>O 0.649580466 0.878554303 0.508010557</div><div><br></div><div>K_POINTS (automatic)</div><div> 5 5 5 1 1 1</div></div><div><br></div><div><br></div>
<br><div class="gmail_quote">On Sun, Jul 29, 2012 at 11:27 AM, Matteo Cococcioni <span dir="ltr"><<a href="mailto:matteo@umn.edu" target="_blank">matteo@umn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Peng,<br>
<br>
I'm not very expert of compiling codes. You have to make sure that all<br>
the libraries are linked correctly for the code to work. I assume you<br>
have QE installed on the same computer. You could give a look in the<br>
make.sys to check what is the correct way to link them. If everything<br>
is consistent, then you have to find out where the code is failing.<br>
have you tried to run with n1 = n2 = n3 = 1? what did you get?<br>
<span><font color="#888888"><br>
Matteo<br>
</font></span><div><div><br>
<br>
<br>
On Sat, Jul 28, 2012 at 9:10 PM, Peng Chen <<a href="mailto:pchen@ion.chem.utk.edu" target="_blank">pchen@ion.chem.utk.edu</a>> wrote:<br>
> Dear Dr. Matteo,<br>
><br>
> I used command listed below to compile resp_mat.f90. No error in compiling.<br>
> I am not sure if I did right in choosing the libs.<br>
> ifort -o r.x resp_mat.f90 -L"/data/apps/intel/11.1.072/mkl/lib/em64t"<br>
> -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_mc3 -lmkl_sequential -lmkl_core<br>
><br>
> The libs in mkl are shown below:<br>
> libmkl_avx.so libmkl_intel_sp2dp.so<br>
> libmkl_blacs_ilp64.a libmkl_intel_thread.a<br>
> libmkl_blacs_intelmpi_ilp64.a libmkl_intel_thread.so<br>
> libmkl_blacs_intelmpi_ilp64.so libmkl_lapack95_ilp64.a<br>
> libmkl_blacs_intelmpi_lp64.a libmkl_lapack95_lp64.a<br>
> libmkl_blacs_intelmpi_lp64.so libmkl_lapack.so<br>
> libmkl_blacs_lp64.a libmkl_mc3.so<br>
> libmkl_blacs_openmpi_ilp64.a libmkl_mc.so<br>
> libmkl_blacs_openmpi_lp64.a libmkl_p4n.so<br>
> libmkl_blacs_sgimpt_ilp64.a libmkl_pgi_thread.a<br>
> libmkl_blacs_sgimpt_lp64.a libmkl_pgi_thread.so<br>
> libmkl_blas95_ilp64.a libmkl_scalapack_ilp64.a<br>
> libmkl_blas95_lp64.a libmkl_scalapack_ilp64.so<br>
> libmkl_cdft_core.a libmkl_scalapack_lp64.a<br>
> libmkl_core.a libmkl_scalapack_lp64.so<br>
> libmkl_core.so libmkl_sequential.a<br>
> libmkl_def.so libmkl_sequential.so<br>
> libmkl_gf_ilp64.a libmkl_solver_ilp64.a<br>
> libmkl_gf_ilp64.so libmkl_solver_ilp64_sequential.a<br>
> libmkl_gf_lp64.a libmkl_solver_lp64.a<br>
> libmkl_gf_lp64.so libmkl_solver_lp64_sequential.a<br>
> libmkl_gnu_thread.a libmkl_vml_avx.so<br>
> libmkl_gnu_thread.so libmkl_vml_def.so<br>
> libmkl_intel_ilp64.a libmkl_vml_mc2.so<br>
> libmkl_intel_ilp64.so libmkl_vml_mc3.so<br>
> libmkl_intel_lp64.a libmkl_vml_mc.so<br>
> libmkl_intel_lp64.so libmkl_vml_p4n.so<br>
> libmkl_intel_sp2dp.a locale<br>
><br>
><br>
> Some errors in output:<br>
> forrtl: severe (174): SIGSEGV, segmentation fault occurred<br>
> Image PC Routine Line Source<br>
> r.x 0000000000445659 Unknown Unknown Unknown<br>
> r.x 000000000040A363 Unknown Unknown Unknown<br>
> r.x 000000000040338C Unknown Unknown Unknown<br>
> libc.so.6 00002B85B9495994 Unknown Unknown Unknown<br>
> r.x 0000000000403289 Unknown Unknown Unknown<br>
><br>
><br>
> On Sat, Jul 28, 2012 at 10:38 AM, Matteo Cococcioni <<a href="mailto:matteo@umn.edu" target="_blank">matteo@umn.edu</a>> wrote:<br>
>><br>
>> Dear Peng,<br>
>><br>
>> nothing looks wrong in your input. have you tried with n1, n2, n3 all<br>
>> equal to 1? are you sure you compiled correctly?<br>
>><br>
>> Matteo<br>
>><br>
>><br>
>><br>
>> On Fri, Jul 27, 2012 at 11:46 PM, Peng Chen <<a href="mailto:pchen@ion.chem.utk.edu" target="_blank">pchen@ion.chem.utk.edu</a>><br>
>> wrote:<br>
>> > Dear Dr. Matteo,<br>
>> ><br>
>> > The primitive cell has 26 atoms with 3 different types. The pos and<br>
>> > <a href="http://resp_mat.in" target="_blank">resp_mat.in</a> files are shown below:<br>
>> ><br>
>> > 5.6087 10.79 0.0<br>
>> > 5.6087 -10.79 0.0<br>
>> > 0.0 0.0 15.570873<br>
>> > 0 0 0 1<br>
>> > 0.5 0.5 0.5 -1<br>
>> > 0.12286329 0.378190177 0.749934361 1<br>
>> > 0.87713671 0.621809823 0.250065639 1<br>
>> > 0.377137388 0.121809201 0.249932658 -1<br>
>> > 0.622862612 0.878190799 0.750067342 -1<br>
>> > 0.373618754 0.623612138 0.11586798 0<br>
>> > 0.126381501 0.876388862 0.615868582 0<br>
>> > 0.626381246 0.376387862 0.88413202 0<br>
>> > 0.873618499 0.123611138 0.384131418 0<br>
>> > 0.241839036 0.756304999 0.223613779 0<br>
>> > 0.258160617 0.74369391 0.723611944 0<br>
>> > 0.758160964 0.243695001 0.776386221 0<br>
>> > 0.741839383 0.25630609 0.276388056 0<br>
>> > -0.000998332 1.000227439 0.243205274 0<br>
>> > 0.500997862 0.499772508 0.743208489 0<br>
>> > 1.000998332 -0.000227439 0.756794726 0<br>
>> > 0.499002138 0.500227492 0.256791511 0<br>
>> > 0.381099639 0.150692971 0.006796703 0<br>
>> > 0.118898786 0.349304325 0.506798051 0<br>
>> > 0.149581603 0.378555571 0.991989919 0<br>
>> > 0.350419534 0.121445697 0.491991443 0<br>
>> > 0.618900361 0.849307029 0.993205297 0<br>
>> > 0.881101214 0.650695675 0.493203949 0<br>
>> > 0.850418397 0.621444429 0.008012081 0<br>
>> > 0.649580466 0.878554303 0.508010557 0<br>
>> ><br>
>> > <a href="http://resp_mat.in" target="_blank">resp_mat.in</a> :<br>
>> > &input_mat<br>
>> > ntyp = 3<br>
>> > na(1) = 6<br>
>> > na(2) = 4<br>
>> > na(3) = 16<br>
>> > nalfa = 5<br>
>> > magn=.true.<br>
>> > filepos = 'pos'<br>
>> > back = 'no'<br>
>> > filednda = 'file_afm'<br>
>> > n1 = 2<br>
>> > n2 = 2<br>
>> > n3 = 2<br>
>> > &end<br>
>> ><br>
>> ><br>
>> ><br>
>> > On Fri, Jul 27, 2012 at 3:02 PM, Matteo Cococcioni <<a href="mailto:matteo@umn.edu" target="_blank">matteo@umn.edu</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Dear Peng,<br>
>> >><br>
>> >> can you provide info about your system? maybe it is larger than the<br>
>> >> maximum size allowed by r.x?<br>
>> >><br>
>> >> Matteo<br>
>> >><br>
>> >> On Fri, Jul 27, 2012 at 12:41 PM, Peng Chen <<a href="mailto:pchen@ion.chem.utk.edu" target="_blank">pchen@ion.chem.utk.edu</a>><br>
>> >> wrote:<br>
>> >> > Dear All,<br>
>> >> ><br>
>> >> > There are some errors when I run r.x to calculate the U. I used<br>
>> >> > Espresso-5.0<br>
>> >> > and follow the steps in LSDA+U example. I am not sure what could be<br>
>> >> > wrong.<br>
>> >> > And if you need other input/output, please let me know.<br>
>> >> ><br>
>> >> > Image PC Routine Line Source<br>
>> >> > r.x 0822DACC Unknown Unknown Unknown<br>
>> >> > r.x 0822C265 Unknown Unknown Unknown<br>
>> >> > r.x 082071FA Unknown Unknown Unknown<br>
>> >> > r.x 081DDFDA Unknown Unknown Unknown<br>
>> >> > r.x 081FA33B Unknown Unknown Unknown<br>
>> >> > r.x 081F9C5C Unknown Unknown Unknown<br>
>> >> > r.x 0804E38F Unknown Unknown Unknown<br>
>> >> > r.x 0804824A Unknown Unknown Unknown<br>
>> >> > r.x 0823805D Unknown Unknown Unknown<br>
>> >> > r.x 08048131 Unknown Unknown Unknown<br>
>> >> > forrtl: severe (8): internal consistency check failure, file<br>
>> >> > ./src/libfor/for_wseq_lis.c, line 635<br>
>> >> > Image PC Routine Line Source<br>
>> >> > r.x 0822DACC Unknown Unknown Unknown<br>
>> >> > r.x 0822C265 Unknown Unknown Unknown<br>
>> >> > r.x 082071FA Unknown Unknown Unknown<br>
>> >> > r.x 081DD664 Unknown Unknown Unknown<br>
>> >> > r.x 081F9AF7 Unknown Unknown Unknown<br>
>> >> > r.x 0804E38F Unknown Unknown Unknown<br>
>> >> > r.x 0804824A Unknown Unknown Unknown<br>
>> >> > r.x 0823805D Unknown Unknown Unknown<br>
>> >> > r.x 08048131 Unknown Unknown Unknown<br>
>> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred<br>
>> >> > Image PC Routine Line Source<br>
>> >> > r.x 0804DAED Unknown Unknown Unknown<br>
>> >> > r.x 0804824A Unknown Unknown Unknown<br>
>> >> > r.x 0823805D Unknown Unknown Unknown<br>
>> >> > r.x 08048131 Unknown Unknown Unknown<br>
>> >> > forrtl: severe (174): SIGSEGV, segmentation fault occurred<br>
>> >> > Image PC Routine Line Source<br>
>> >> > r.x 08253657 Unknown Unknown Unknown<br>
>> >> > r.x 081F4087 Unknown Unknown Unknown<br>
>> >> > r.x 081DCDB7 Unknown Unknown Unknown<br>
>> >> > r.x 081DF354 Unknown Unknown Unknown<br>
>> >> > r.x 081DD672 Unknown Unknown Unknown<br>
>> >> > r.x 081DF5E8 Unknown Unknown Unknown<br>
>> >> > Unknown FFFFE600 Unknown Unknown Unknown<br>
>> >> > r.x 0804824A Unknown Unknown Unknown<br>
>> >> > r.x 0823805D Unknown Unknown Unknown<br>
>> >> > r.x 08048131 Unknown Unknown Unknown<br>
>> >> ><br>
>> >> ><br>
>> >> > --<br>
>> >> > Best Regards.<br>
>> >> > Peng<br>
>> >> ><br>
>> >> > _______________________________________________<br>
>> >> > Pw_forum mailing list<br>
>> >> > <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
>> >> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
>> >> ><br>
>> >><br>
>> >><br>
>> >><br>
>> >> --<br>
>> >> Matteo Cococcioni<br>
>> >> Department of Chemical Engineering and Materials Science,<br>
>> >> University of Minnesota<br>
>> >> 421 Washington Av. SE<br>
>> >> Minneapolis, MN 55455<br>
>> >> Tel. <a href="tel:%2B1%20612%20624%209056" value="+16126249056" target="_blank">+1 612 624 9056</a> Fax <a href="tel:%2B1%20612%20626%207246" value="+16126267246" target="_blank">+1 612 626 7246</a><br>
>> >> _______________________________________________<br>
>> >> Pw_forum mailing list<br>
>> >> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
>> >> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > --<br>
>> > Best Regards.<br>
>> > Peng<br>
>> ><br>
>> > _______________________________________________<br>
>> > Pw_forum mailing list<br>
>> > <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
>> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Matteo Cococcioni<br>
>> Department of Chemical Engineering and Materials Science,<br>
>> University of Minnesota<br>
>> 421 Washington Av. SE<br>
>> Minneapolis, MN 55455<br>
>> Tel. <a href="tel:%2B1%20612%20624%209056" value="+16126249056" target="_blank">+1 612 624 9056</a> Fax <a href="tel:%2B1%20612%20626%207246" value="+16126267246" target="_blank">+1 612 626 7246</a><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
>> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Best Regards.<br>
> Peng<br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
> <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>
><br>
<br>
<br>
<br>
--<br>
Matteo Cococcioni<br>
Department of Chemical Engineering and Materials Science,<br>
University of Minnesota<br>
421 Washington Av. SE<br>
Minneapolis, MN 55455<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br> Best Regards.<br> Peng <br>
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