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Fatal error in NEGF run Date: 2017/02/21 15:41 Name: Andy   <And.chuck.phy@gmail.com> Dear Prof. Ozaki and Experts, I have successfully done the transport calculation in the zigzag graphene nanoribbon without any error. Now, I want to do the transport calculations in the Armchair graphene nanoribbon. I ran both of the leads successfully. When I ran the NEGF file, it gives the fatal error mentioned below: ./negf-7agnr-0.0.tranec0_0_1_3_r.cube ./negf-7agnr-0.0.tranec0_0_1_3_i.cube ./negf-7agnr-0.0.tranec0_0_1_4_r.cube ./negf-7agnr-0.0.tranec0_0_1_4_i.cube [localhost:11972] *** Process received signal *** [localhost:11973] *** Process received signal *** [localhost:11973] Signal: Segmentation fault (11) [localhost:11973] Signal code: Address not mapped (1) [localhost:11973] Failing at address: 0x19 [localhost:11972] Signal: Segmentation fault (11) [localhost:11972] Signal code: Address not mapped (1) [localhost:11972] Failing at address: 0x19 [localhost:11974] *** Process received signal *** [localhost:11974] Signal: Segmentation fault (11) [localhost:11974] Signal code: Address not mapped (1) [localhost:11974] Failing at address: 0x19 ............................. ............................. ............................. [localhost:11973] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0] [localhost:11973] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365] [localhost:11973] [ 2] openmx [0x6ebefd] [localhost:11973] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511] [localhost:11973] [ 4] openmx(main+0xddc) [0x430f14] [localhost:11974] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0] [localhost:11974] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365] [localhost:11974] [ 2] openmx [0x6ebefd] [localhost:11974] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511] [localhost:11974] [ 4] openmx(main+0xddc) [0x430f14] [localhost:11974] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb] [localhost:11974] [ 6] openmx [0x4300aa] [localhost:11974] *** End of error message *** [localhost:11973] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb] [localhost:11973] [ 6] openmx [0x4300aa] [localhost:11973] *** End of error message *** [localhost:11972] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0] [localhost:11972] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365] [localhost:11972] [ 2] openmx [0x6ebefd] [localhost:11972] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511] [localhost:11972] [ 4] openmx(main+0xddc) [0x430f14] [localhost:11972] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb] [localhost:11972] [ 6] openmx [0x4300aa] [localhost:11972] *** End of error message *** [localhost:11984] *** Process received signal *** [localhost:11984] Signal: Segmentation fault (11) [localhost:11984] Signal code: Address not mapped (1) [localhost:11984] Failing at address: 0x19 [localhost:11984] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0] [localhost:11984] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365] [localhost:11984] [ 2] openmx [0x6ebefd] [localhost:11984] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511] [localhost:11984] [ 4] openmx(main+0xddc) [0x430f14] [localhost:11984] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb] [localhost:11984] [ 6] openmx [0x4300aa] [localhost:11984] *** End of error message *** [localhost:11965] *** Process received signal *** [localhost:11965] Signal: Segmentation fault (11) [localhost:11965] Signal code: Address not mapped (1) [localhost:11965] Failing at address: 0x19 I am not able to resolve this error. Can you please help me to get rid of this. Your help would be highly appreciated. best, Chuck

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Re: Fatal error in NEGF run ( No.1 ) Date: 2017/03/02 19:12 Name: T. Ozaki Hi, I did calculations with input files: Lead-L-8ZGNR.dat Lead-R-8ZGNR.dat NEGF-8ZGNR-0.3.dat which are stored in work/negf_example. I confirmed that all the calculations finished normally. On the other hand, the error message you had implies that the error appeared in the part related to the eigenchannel analysis. Actually, the functionality has been newly added from Ver. 3.8. So it is likely that there is a program bug in the newly developed part. If you do not mind, could you post your input files so that I can check possible bugs? Thank you for your cooperation in advance. Regards, TO Re: Fatal error in NEGF run ( No.2 ) Date: 2017/03/07 23:52 Name: Fronquer Dear Prof. Ozaki, Thank you for your reply. I am pasting here my input files. Three input files are very large so I am pasting SCF electronic system parameters and NEGF file that contains the left and right lead and a central region. Species.Number 2 <Definition.of.Atomic.Species C C5.0-s2p1 C_CA13 H H5.0-s2 H_CA13 Definition.of.Atomic.Species> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 0.000 0.000 8.53 10.000 0.000 0.000 0.000 27.000 0.000 Atoms.UnitVectors> # # SCF or Electronic System # scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization on # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 120.0 # default=150 (Ry) #scf.Ngrid 140 140 100 # about=200 (Ry) scf.maxIter 1000 # default=40 scf.EigenvalueSolver Band # DC|GDC|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 201 1 1 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Kerker.factor 10.0 # default=1 scf.Init.Mixing.Weight 0.001 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.105 # default=0.40 scf.Mixing.History 40 # default=5 scf.Mixing.StartPulay 10 # default=6 scf.Mixing.EveryPulay 1 # default=6 scf.criterion 1.0e-9 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type Nomd # Opt|EF|BFGS|RF|DIIS MD.Opt.DIIS.History 18 # default=3 MD.Opt.StartDIIS 6 # default=5 MD.Opt.EveryDIIS 5 # default=10 MD.maxIter 2000 # MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.) # # Band dispersion # Band.dispersion off # on|off, default=off <Band.KPath.UnitCell 0.000 0.000 4.88 10.000 0.000 0.000 0.000 27.000 0.000 Band.KPath.UnitCell> Band.Nkpath 1 <Band.kpath 601 0.0 0.0 0.0 0.5 0.0 0.0 G X Band.kpath> # # DOS and PDOS # Dos.fileout off # on|off, default=off Dos.Erange -20.0 20.0 # default = -20 20 Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3 _______________________________________________________________________________________ ___________________________________________________________________ NEGF FIle System.CurrrentDirectory ./ # default=./ System.Name negf-7agnr-0.0 level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (0-2) NEGF.filename.hks.l lead-l-7agnr.hks NEGF.filename.hks.r lead-r-7agnr.hks NEGF.SCF.Iter.Band 20 NEGF.Num.Poles 100 # defalut=150 NEGF.scf.Kgrid 1 1 # defalut=1 1 NEGF.bias.voltage 0.0 # default=0.0 (eV) NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV) NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV) Dos.fileout off # on|off, default=off NEGF.Dos.energyrange -20.0 20.0 1.0e-4 #default=-10.0 10.0 5.0e-3 (eV) NEGF.Dos.energy.div 4000 # default=200 NEGF.Dos.Kgrid 1 1 # default=1 1 # # Transmission & Eigen Channel Analysis # NEGF.tran.Analysis on # default on NEGF.tran.energydiv 800 # default=200 NEGF.tran.energyrange -4 4 0.001 # default=-10.0 10.0 5.0e-3 (eV) NEGF.tran.Kgrid 1 1 # default= 1 1 NEGF.tran.CurrentDensity on # default on NEGF.tran.Channel on # default on NEGF.Channel.Nkpoint 1 # default 1 <NEGF.Channel.kpoint 0.0 0.0 NEGF.Channel.kpoint> # default 0.0 0.0 NEGF.Channel.Nenergy 1 # default 1 <NEGF.Channel.energy 0.0 NEGF.Channel.energy> # default 0.0 NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear) # # Definition of Atomic Species # Species.Number 2 <Definition.of.Atomic.Species C C5.0-s2p1 C_CA13 H H5.0-s2 H_CA13 Definition.of.Atomic.Species> # # Atoms # Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU Atoms.Number 30 <Atoms.SpeciesAndCoordinates 1 H 0.00000000 1.49896799 10.45476799 0.50000000 0.50000000 2 H 0.00000000 1.49896799 12.23323212 0.50000000 0.50000000 3 C 0.00000000 2.45111126 9.89602526 2.10000000 1.90000000 4 C 0.00000000 3.66326134 10.62482532 2.10000000 1.90000000 5 C 0.00000000 2.45111126 12.79197487 2.10000000 1.90000000 6 C 0.00000000 3.66326134 12.06317479 2.10000000 1.90000000 7 C 0.00000000 4.89179041 9.91972866 2.10000000 1.90000000 8 C 0.00000000 6.13044410 10.63467848 2.10000000 1.90000000 9 C 0.00000000 4.89179041 12.76827147 2.10000000 1.90000000 10 C 0.00000000 6.13044409 12.05332163 2.10000000 1.90000000 11 C 0.00000000 7.36138815 9.91884466 2.10000000 1.90000000 12 C 0.00000000 8.59083892 10.63036886 2.10000000 1.90000000 13 C 0.00000000 7.36138815 12.76915547 2.10000000 1.90000000 14 C 0.00000000 8.59083892 12.05763127 2.10000000 1.90000000 15 C 0.00000000 9.82419453 9.91415758 2.10000000 1.90000000 16 C 0.00000000 11.05755015 10.63036886 2.10000000 1.90000000 17 C 0.00000000 9.82419453 12.77384254 2.10000000 1.90000000 18 C 0.00000000 11.05755015 12.05763127 2.10000000 1.90000000 19 C 0.00000000 12.28700091 9.91884465 2.10000000 1.90000000 20 C 0.00000000 13.51794496 10.63467848 2.10000000 1.90000000 21 C 0.00000000 12.28700091 12.76915547 2.10000000 1.90000000 22 C 0.00000000 13.51794497 12.05332163 2.10000000 1.90000000 23 C 0.00000000 14.75659866 9.91972865 2.10000000 1.90000000 24 C 0.00000000 15.98512772 10.62482532 2.10000000 1.90000000 25 C 0.00000000 14.75659865 12.76827147 2.10000000 1.90000000 26 C 0.00000000 15.98512773 12.06317479 2.10000000 1.90000000 27 C 0.00000000 17.19727781 9.89602526 2.10000000 1.90000000 28 C 0.00000000 17.19727781 12.79197487 2.10000000 1.90000000 29 H 0.00000000 18.14942107 10.45476800 0.50000000 0.50000000 30 H 0.00000000 18.14942108 12.23323212 0.50000000 0.50000000 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU #<Atoms.UnitVectors # 0.000 0.000 4.88 # 10.000 0.000 0.000 # 0.000 24.000 0.000 #Atoms.UnitVectors> # # Lead-Left # LeftLeadAtoms.Number 60 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 0.00000000 2.37422687 1.36437614 2.50000000 1.50000000 2 C 0.00000000 3.60839082 2.05960208 2.50000000 1.50000000 3 C 0.00000000 2.43376259 4.26115562 2.50000000 1.50000000 4 C 0.00000000 3.63512993 3.52681035 2.50000000 1.50000000 5 C 0.00000000 2.44349640 5.63613271 2.50000000 1.50000000 6 C 0.00000000 3.65991791 6.35381020 2.50000000 1.50000000 7 C 0.00000000 2.45076875 8.52190761 2.50000000 1.50000000 8 C 0.00000000 3.66230931 7.79234988 2.50000000 1.50000000 9 C 0.00000000 4.84318085 1.42797834 2.50000000 1.50000000 10 C 0.00000000 6.10587470 2.04496891 2.50000000 1.50000000 11 C 0.00000000 4.87548695 4.21269140 2.50000000 1.50000000 12 C 0.00000000 6.11332783 3.50164816 2.50000000 1.50000000 13 C 0.00000000 4.88522084 5.64270708 2.50000000 1.50000000 14 C 0.00000000 6.12600371 6.35441190 2.50000000 1.50000000 15 C 0.00000000 4.89180632 8.49445642 2.50000000 1.50000000 16 C 0.00000000 6.12857687 7.77559630 2.50000000 1.50000000 17 C 0.00000000 7.35313902 1.43003935 2.50000000 1.50000000 18 C 0.00000000 8.59714409 2.05896815 2.50000000 1.50000000 19 C 0.00000000 7.35235294 4.20354262 2.50000000 1.50000000 20 C 0.00000000 8.58947845 3.50861616 2.50000000 1.50000000 21 C 0.00000000 7.35570450 5.63863657 2.50000000 1.50000000 22 C 0.00000000 8.58779645 6.34964624 2.50000000 1.50000000 23 C 0.00000000 7.36049316 8.48950565 2.50000000 1.50000000 24 C 0.00000000 8.58955552 7.77723893 2.50000000 1.50000000 25 C 0.00000000 9.82419454 1.35293302 2.50000000 1.50000000 26 C 0.00000000 11.05124499 2.05896815 2.50000000 1.50000000 27 C 0.00000000 9.82419453 4.21523106 2.50000000 1.50000000 28 C 0.00000000 11.05891061 3.50861616 2.50000000 1.50000000 29 C 0.00000000 9.82419453 5.63934129 2.50000000 1.50000000 30 C 0.00000000 11.06059262 6.34964624 2.50000000 1.50000000 31 C 0.00000000 9.82419453 8.49176210 2.50000000 1.50000000 32 C 0.00000000 11.05883355 7.77723893 2.50000000 1.50000000 33 C 0.00000000 12.29525004 1.43003937 2.50000000 1.50000000 34 C 0.00000000 13.54251437 2.04496891 2.50000000 1.50000000 35 C 0.00000000 12.29603613 4.20354261 2.50000000 1.50000000 36 C 0.00000000 13.53506124 3.50164815 2.50000000 1.50000000 37 C 0.00000000 12.29268457 5.63863657 2.50000000 1.50000000 38 C 0.00000000 13.52238535 6.35441190 2.50000000 1.50000000 39 C 0.00000000 12.28789590 8.48950564 2.50000000 1.50000000 40 C 0.00000000 13.51981219 7.77559630 2.50000000 1.50000000 41 C 0.00000000 14.80520821 1.42797831 2.50000000 1.50000000 42 C 0.00000000 16.03999827 2.05960209 2.50000000 1.50000000 43 C 0.00000000 14.77290213 4.21269140 2.50000000 1.50000000 44 C 0.00000000 16.01325914 3.52681034 2.50000000 1.50000000 45 C 0.00000000 14.76316823 5.64270708 2.50000000 1.50000000 46 C 0.00000000 15.98847116 6.35381019 2.50000000 1.50000000 47 C 0.00000000 14.75658274 8.49445642 2.50000000 1.50000000 48 C 0.00000000 15.98607975 7.79234988 2.50000000 1.50000000 49 C 0.00000000 17.27416221 1.36437613 2.50000000 1.50000000 50 C 0.00000000 17.21462647 4.26115561 2.50000000 1.50000000 51 C 0.00000000 17.20489266 5.63613270 2.50000000 1.50000000 52 C 0.00000000 17.19762032 8.52190761 2.50000000 1.50000000 53 H 0.00000000 1.58490677 2.17980351 0.50000000 0.50000000 54 H 0.00000000 1.48154811 3.69397693 0.50000000 0.50000000 55 H 0.00000000 1.49586602 6.20324257 0.50000000 0.50000000 56 H 0.00000000 1.49842826 7.96335252 0.50000000 0.50000000 57 H 0.00000000 18.06348229 2.17980351 0.50000000 0.50000000 58 H 0.00000000 18.16684095 3.69397694 0.50000000 0.50000000 59 H 0.00000000 18.15252305 6.20324258 0.50000000 0.50000000 60 H 0.00000000 18.14996080 7.96335253 0.50000000 0.50000000 LeftLeadAtoms.SpeciesAndCoordinates> # # Lead-Right # RightLeadAtoms.Number 60 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 H 0.00000000 1.49842826 14.72464760 0.50000000 0.50000000 2 H 0.00000000 1.49586602 16.48475754 0.50000000 0.50000000 3 H 0.00000000 1.48154811 18.99402317 0.50000000 0.50000000 4 H 0.00000000 1.58490676 20.50819659 0.50000000 0.50000000 5 C 0.00000000 2.45076875 14.16609249 1.50000000 2.50000000 6 C 0.00000000 3.66230931 14.89565025 1.50000000 2.50000000 7 C 0.00000000 2.44349640 17.05186740 1.50000000 2.50000000 8 C 0.00000000 3.65991791 16.33418993 1.50000000 2.50000000 9 C 0.00000000 2.43376259 18.42684451 1.50000000 2.50000000 10 C 0.00000000 3.63512993 19.16118977 1.50000000 2.50000000 11 C 0.00000000 2.37422685 21.32362399 1.50000000 2.50000000 12 C 0.00000000 3.60839080 20.62839803 1.50000000 2.50000000 13 C 0.00000000 4.89180632 14.19354369 1.50000000 2.50000000 14 C 0.00000000 6.12857687 14.91240382 1.50000000 2.50000000 15 C 0.00000000 4.88522084 17.04529304 1.50000000 2.50000000 16 C 0.00000000 6.12600371 16.33358822 1.50000000 2.50000000 17 C 0.00000000 4.87548694 18.47530872 1.50000000 2.50000000 18 C 0.00000000 6.11332783 19.18635197 1.50000000 2.50000000 19 C 0.00000000 4.84318085 21.26002178 1.50000000 2.50000000 20 C 0.00000000 6.10587470 20.64303121 1.50000000 2.50000000 21 C 0.00000000 7.36049316 14.19849447 1.50000000 2.50000000 22 C 0.00000000 8.58955552 14.91076119 1.50000000 2.50000000 23 C 0.00000000 7.35570450 17.04936355 1.50000000 2.50000000 24 C 0.00000000 8.58779645 16.33835388 1.50000000 2.50000000 25 C 0.00000000 7.35235294 18.48445751 1.50000000 2.50000000 26 C 0.00000000 8.58947845 19.17938397 1.50000000 2.50000000 27 C 0.00000000 7.35313902 21.25796078 1.50000000 2.50000000 28 C 0.00000000 8.59714408 20.62903197 1.50000000 2.50000000 29 C 0.00000000 9.82419453 14.19623802 1.50000000 2.50000000 30 C 0.00000000 11.05883355 14.91076119 1.50000000 2.50000000 31 C 0.00000000 9.82419453 17.04865884 1.50000000 2.50000000 32 C 0.00000000 11.06059262 16.33835388 1.50000000 2.50000000 33 C 0.00000000 9.82419453 18.47276907 1.50000000 2.50000000 34 C 0.00000000 11.05891061 19.17938397 1.50000000 2.50000000 35 C 0.00000000 9.82419453 21.33506711 1.50000000 2.50000000 36 C 0.00000000 11.05124498 20.62903197 1.50000000 2.50000000 37 C 0.00000000 12.28789590 14.19849448 1.50000000 2.50000000 38 C 0.00000000 13.51981220 14.91240382 1.50000000 2.50000000 39 C 0.00000000 12.29268456 17.04936355 1.50000000 2.50000000 40 C 0.00000000 13.52238536 16.33358822 1.50000000 2.50000000 41 C 0.00000000 12.29603613 18.48445751 1.50000000 2.50000000 42 C 0.00000000 13.53506124 19.18635197 1.50000000 2.50000000 43 C 0.00000000 12.29525005 21.25796078 1.50000000 2.50000000 44 C 0.00000000 13.54251437 20.64303122 1.50000000 2.50000000 45 C 0.00000000 14.75658274 14.19354369 1.50000000 2.50000000 46 C 0.00000000 15.98607976 14.89565025 1.50000000 2.50000000 47 C 0.00000000 14.76316823 17.04529304 1.50000000 2.50000000 48 C 0.00000000 15.98847116 16.33418992 1.50000000 2.50000000 49 C 0.00000000 14.77290212 18.47530872 1.50000000 2.50000000 50 C 0.00000000 16.01325915 19.16118977 1.50000000 2.50000000 51 C 0.00000000 14.80520823 21.26002178 1.50000000 2.50000000 52 C 0.00000000 16.03999826 20.62839804 1.50000000 2.50000000 53 C 0.00000000 17.19762032 14.16609249 1.50000000 2.50000000 54 C 0.00000000 17.20489267 17.05186740 1.50000000 2.50000000 55 C 0.00000000 17.21462648 18.42684451 1.50000000 2.50000000 56 C 0.00000000 17.27416222 21.32362398 1.50000000 2.50000000 57 H 0.00000000 18.14996080 14.72464760 0.50000000 0.50000000 58 H 0.00000000 18.15252305 16.48475753 0.50000000 0.50000000 59 H 0.00000000 18.16684096 18.99402318 0.50000000 0.50000000 60 H 0.00000000 18.06348230 20.50819661 0.50000000 0.50000000 RightLeadAtoms.SpeciesAndCoordinates> # # SCF or Electronic System # scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization on # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 120.0 # default=150 (Ry) #scf.Ngrid 140 140 100 # about=200 (Ry) scf.maxIter 2000 # default=40 scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr scf.Kgrid 1 1 1 # means n1 x n2 x n3 scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Kerker.factor 20.0 # default=1 scf.Init.Mixing.Weight 0.1 # default=0.30 scf.Min.Mixing.Weight 0.04 # default=0.001 scf.Max.Mixing.Weight 0.4 # default=0.40 scf.Mixing.History 60 # default=5 scf.Mixing.StartPulay 20 # default=6 scf.Mixing.EveryPulay 1 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type Nomd # Opt|EF|BFGS|RF|DIIS MD.Opt.DIIS.History 10 # default=3 MD.Opt.StartDIIS 6 # default=5 MD.Opt.EveryDIIS 5 # default=10 MD.maxIter 200 # MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.) Please have a look and help me in overcoming to this problem. Thanking you. Re: Fatal error in NEGF run ( No.3 ) Date: 2017/03/08 14:59 Name: T. Ozaki Hi, It turned out that this is actually caused by a bug that memory deallocation is improperly performed in TRAN_Main_Analysis.c. The bug has been fixed and the patch is available as patch3.8.3.tar.gz at http://www.openmx-square.org/download.html Thank you for your feedback and cooperation. Regards, TO Re: Fatal error in NEGF run ( No.4 ) Date: 2017/03/14 07:01 Name: ali i have the same problem and i use the new patch but the problem exist. Re: Fatal error in NEGF run ( No.5 ) Date: 2017/03/14 15:36 Name: ali Dear developers i applied new patch but the bug did not fixed? what should i do? thanks Re: Fatal error in NEGF run ( No.6 ) Date: 2017/03/14 15:54 Name: T. Ozaki Hi, If you do not mind, cloud you share your input files which caused the problem? Regards, TO P.S. The problem does not cause serious trouble for your final results, since this happens at the end of the code where memory deallocations are performed. Re: Fatal error in NEGF run ( No.7 ) Date: 2017/03/14 16:47 Name: ali hi System.CurrrentDirectory ./ # default=./ System.Name ngf-0.0 level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (0-2) # # Definition of Atomic Species # Species.Number 2 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_CA13 N N5.0-s2p2d1 N_CA13 Definition.of.Atomic.Species> NEGF.filename.hks.l lead.hks NEGF.filename.hks.r lead.hks NEGF.Num.Poles 100 # defalut=150 NEGF.scf.Kgrid 1 1 # defalut=1 1 NEGF.bias.voltage 0.0 # default=0.0 (eV) NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV) NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV) NEGF.scf.Iter.Band 20 NEGF.tran.energydiv 200 # default=200 NEGF.tran.energyrange -10.0 10.0 5.0e-3 # default=-10.0 10.0 5.0e-3 (eV) NEGF.tran.Kgrid 1 1 # default= 1 1 Atoms.Number 29 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C 9.2009321 3.0665410 7.6944084 2.00000 2.00000 2 C 9.2180813 0.6127711 7.6910203 2.00000 2.00000 3 C 9.9230181 1.8475303 7.6879522 2.00000 2.00000 4 C 9.9222386 4.2852240 7.6842867 2.00000 2.00000 5 C 11.3356511 1.7893617 7.6782112 2.00000 2.00000 6 C 11.3348041 4.3424755 7.6707664 2.00000 2.00000 7 N 11.9517960 0.6112769 7.6639009 2.50000 2.50000 8 N 12.0784601 3.0675667 7.6825771 2.50000 2.50000 9 C 13.4989073 3.0651358 7.7596100 2.00000 2.00000 10 N 14.1548404 4.2277609 7.6536692 2.50000 2.50000 11 N 14.1140825 1.8949232 7.9088371 2.50000 2.50000 12 C 15.4019534 4.2073312 8.0919982 2.00000 2.00000 13 C 15.4019771 1.9312983 8.1752629 2.00000 2.00000 14 N 16.0456234 3.0821314 8.4735999 2.50000 2.50000 15 N 16.1088921 0.6147233 8.1460947 2.50000 2.50000 16 C 17.5282627 0.6148996 8.0504150 2.00000 2.00000 17 N 18.1540095 1.7842448 8.0857851 2.50000 2.50000 18 N 18.1650615 4.3606991 7.8678134 2.50000 2.50000 19 C 19.4633695 1.7518032 8.2416761 2.00000 2.00000 20 C 19.4549595 4.3821546 8.1696274 2.00000 2.00000 21 N 20.1267445 0.6017957 8.4869103 2.50000 2.50000 22 N 20.1664314 3.0667473 8.1521931 2.50000 2.50000 23 C 21.5731076 3.0686110 7.9471351 2.00000 2.00000 24 N 22.1939245 4.2309451 7.7344599 2.50000 2.50000 25 N 22.2143785 1.9029856 7.9558298 2.50000 2.50000 26 C 23.4932174 4.2748061 7.7166978 2.00000 2.00000 27 C 23.5018150 1.8598120 7.8001596 2.00000 2.00000 28 N 24.2570850 3.0673182 7.7406987 2.50000 2.50000 29 N 24.1886586 0.6123005 7.7060660 2.50000 2.50000 Atoms.SpeciesAndCoordinates> LeftLeadAtoms.Number 16 <LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 0.7083626 3.0673063 7.7029471 2.00000 2.00000 2 C 0.7083626 0.6134413 7.7029454 2.00000 2.00000 3 C 1.4166265 1.8404224 7.7029714 2.00000 2.00000 4 C 1.4166265 4.2942874 7.7029712 2.00000 2.00000 5 C 2.8334116 1.8404223 7.7029785 2.00000 2.00000 6 C 2.8334116 4.2942873 7.7029795 2.00000 2.00000 7 C 3.5416756 0.6134413 7.7029482 2.00000 2.00000 8 C 3.5416756 3.0673062 7.7029482 2.00000 2.00000 9 C 4.9584126 3.0673063 7.7029371 2.00000 2.00000 10 C 4.9584126 0.6134413 7.7029354 2.00000 2.00000 11 C 5.6666765 1.8404224 7.7029614 2.00000 2.00000 12 C 5.6666765 4.2942874 7.7029612 2.00000 2.00000 13 C 7.0834616 1.8404223 7.7029685 2.00000 2.00000 14 C 7.0834616 4.2942873 7.7029695 2.00000 2.00000 15 C 7.7917256 0.6134413 7.7029382 2.00000 2.00000 16 C 7.7917256 3.0673062 7.7029382 2.00000 2.00000 LeftLeadAtoms.SpeciesAndCoordinates> # # Lead-Right # RightLeadAtoms.Number 16 <RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang. 1 C 25.6357771 3.0673063 7.7029171 2.00000 2.00000 2 C 25.6357771 0.6134413 7.7029154 2.00000 2.00000 3 C 26.3440410 1.8404224 7.7029414 2.00000 2.00000 4 C 26.3440410 4.2942874 7.7029412 2.00000 2.00000 5 C 27.7608261 1.8404223 7.7029485 2.00000 2.00000 6 C 27.7608261 4.2942873 7.7029495 2.00000 2.00000 7 C 28.4690901 0.6134413 7.7029182 2.00000 2.00000 8 C 28.4690901 3.0673062 7.7029182 2.00000 2.00000 9 C 29.8858271 3.0673063 7.7029071 2.00000 2.00000 10 C 29.8858271 0.6134413 7.7029054 2.00000 2.00000 11 C 30.5940910 1.8404224 7.7029314 2.00000 2.00000 12 C 30.5940910 4.2942874 7.7029312 2.00000 2.00000 13 C 32.0108761 1.8404223 7.7029385 2.00000 2.00000 14 C 32.0108761 4.2942873 7.7029395 2.00000 2.00000 15 C 32.7191401 0.6134413 7.7029082 2.00000 2.00000 16 C 32.7191401 3.0673062 7.7029082 2.00000 2.00000 RightLeadAtoms.SpeciesAndCoordinates> # # SCF or Electronic System # scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 150.0 # default=150 (Ry) scf.maxIter 1000 # default=40 scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band scf.Kgrid 1 1 1 # means n1 x n2 x n3 scf.ProExpn.VNA on # default=on scf.lapack.dste dstevx # dstegr|dstedc|dstevx, scf.Mixing.Type Rmm-Diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.1 # default=0.30 scf.Min.Mixing.Weight 0.001 # default=0.001 scf.Max.Mixing.Weight 0.400 # default=0.40 #scf.Kerker.factor 1.0 # default=1.0 scf.Mixing.History 5 # default=5 scf.Mixing.StartPulay 6 # default=6 scf.Mixing.EveryPulay 5 # default=5 scf.criterion 1.0e-6 # default=1.0e-6 (Hartree) and the error Parameters for the integration of the non-equilibrium part lower bound: -3.607282740421 (eV) upper bound: -3.607282740421 (eV) energy step: 0.020000000000 (eV) number of steps: 0 Warning: the energy step you specified is larger than the integration range. [mmhs:02848] *** Process received signal *** [mmhs:02848] Signal: Segmentation fault (11) [mmhs:02848] Signal code: Address not mapped (1) [mmhs:02848] Failing at address: 0x29 [mmhs:02848] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330) [0x7fa870106330] [mmhs:02848] [ 1] openmx() [0x6875ba] [mmhs:02848] [ 2] openmx() [0x4177e1] [mmhs:02848] [ 3] openmx() [0x43b188] [mmhs:02848] [ 4] openmx() [0x408783] [mmhs:02848] [ 5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fa86fd52f45] [mmhs:02848] [ 6] openmx() [0x4096f5] [mmhs:02848] *** End of error message *** Segmentation fault Re: Fatal error in NEGF run ( No.8 ) Date: 2017/03/14 17:56 Name: T. Ozaki Hi, Please share all the input files for left and right reads and NEGF calculations. Otherwise, it is difficult to reproduce your problem. Regards, TO Re: Fatal error in NEGF run ( No.9 ) Date: 2017/03/15 02:47 Name: ali Dear Prof. Ozaki The bug fixed. I had a mistake in lead file. thank you for your support and guidance. Re: Fatal error in NEGF run ( No.10 ) Date: 2017/03/14 18:55 Name: Fronquer Dear Prof. Ozaki, I have successfully installed the patch and the problem is fixed. Thanks a lot. Regards, Fronquer

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