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Incomplete NEGF run with correct transmission vs energy result Date: 2016/07/19 19:29 Name: Vipin Kumar Dear Openmx experts, I am doing AGNR transport calculation of published work. I am taking all the parameters defined in the published work. I ran left and right lead successfully. When I am running NEGF for transport calculation, I am getting the following error, however, I am getting correct "transmission vs energy" as in the published work. Also it is not generating bulk.xyz file, it may be because of incomplete run. Welcome to TRAN_Main_Analysis. This is a post-processing code of OpenMX to analyze transport properties such as electronic transmission, current, eigen channel, and current distribution in real space based on NEGF. Copyright (C), 2002-2015, H. Kino and T. Ozaki TRAN_Main_Analysis comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under the constitution of the GNU-GPL. ******************************************************* ******************************************************* Chemical potentials used in the SCF calculation Left lead: -4.687615646630 (eV) Right lead: -4.691086407540 (eV) TRAN_Channel_kpoint 0 0.000000 0.000000 TRAN_Channel_energy 0 0.000000 eV TRAN_Channel_Num 5 Parameters for the calculation of the current lower bound: -5.114351027085 (eV) upper bound: -4.264351027085 (eV) energy step: 0.010000000000 (eV) imaginary energy 0.001000000000 (eV) number of steps: 84 calculating... myid0=29 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 myid0= 0 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 myid0= 9 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 myid0=11 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 ........ myid0=28 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 myid0=15 i2= 0 i3= 0 k2= 0.0000 k3= -0.0000 Transmission: files ./negf-agnr0.0.tran0_0 Current: file ./negf-agnr0.0.current Conductance: file ./negf-agnr0.0.conductance Currentdensity: file Start Calculation of the currentdensity Spin #0 Sum of current in real space [Ampere] Left: -4.43369e-14 Right: -4.43369e-14 Spin #1 Sum of current in real space [Ampere] Left: -4.43369e-14 Right: -4.43369e-14 Output: Currentdensity [a.u.] Charge-current density along a-axis: ./negf-agnr0.0.curden1.cube Spin-current density along a-axis: ./negf-agnr0.0.scurden1.cube Charge-current density: ./negf-agnr0.0.curden.xsf Spin-current density: ./negf-agnr0.0.scurden.xsf Voronoi Charge-current density: ./negf-agnr0.0.curden_atom.xsf Voronoi Spin-current density: ./negf-agnr0.0.scurden_atom.xsf ************************************************** Calculation of transmission eigenchannels starts ************************************************** File index : negf-agnr0.0.traneval#k_#E_#spin negf-agnr0.0.tranevec#k_#E_#spin myid0 = 1, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 26, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 4, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 19, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 14, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 6, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 30, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 11, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 12, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 24, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 15, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 9, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 2, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 31, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 13, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 28, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 23, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 17, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 16, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 22, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 29, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 5, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 21, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 8, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 18, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 27, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 20, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 0, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 25, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 7, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 3, #k : 0, N_{ort} / N_{nonort} : 966 / 966 myid0 = 10, #k : 0, N_{ort} / N_{nonort} : 966 / 966 Eigenchannel calculation finished They are written in plottable files. File index : negf-agnr0.0.tranec#k_#E_#spin_#branch_r.cube(.bin) negf-agnr0.0.tranec#k_#E_#spin_#branch_i.cube(.bin) ./negf-agnr0.0.tranec0_0_0_0_r.cube ./negf-agnr0.0.tranec0_0_0_0_i.cube ./negf-agnr0.0.tranec0_0_0_1_r.cube ./negf-agnr0.0.tranec0_0_0_1_i.cube ./negf-agnr0.0.tranec0_0_0_2_r.cube ./negf-agnr0.0.tranec0_0_0_2_i.cube ./negf-agnr0.0.tranec0_0_0_3_r.cube ./negf-agnr0.0.tranec0_0_0_3_i.cube ./negf-agnr0.0.tranec0_0_0_4_r.cube ./negf-agnr0.0.tranec0_0_0_4_i.cube ./negf-agnr0.0.tranec0_0_1_0_r.cube ./negf-agnr0.0.tranec0_0_1_0_i.cube ./negf-agnr0.0.tranec0_0_1_1_r.cube ./negf-agnr0.0.tranec0_0_1_1_i.cube ./negf-agnr0.0.tranec0_0_1_2_r.cube ./negf-agnr0.0.tranec0_0_1_2_i.cube ./negf-agnr0.0.tranec0_0_1_3_r.cube ./negf-agnr0.0.tranec0_0_1_3_i.cube ./negf-agnr0.0.tranec0_0_1_4_r.cube ./negf-agnr0.0.tranec0_0_1_4_i.cube [localhost:05677] *** Process received signal *** [localhost:05677] Signal: Segmentation fault (11) [localhost:05677] Signal code: Address not mapped (1) [localhost:05677] Failing at address: 0x19 [localhost:05692] *** Process received signal *** [localhost:05692] Signal: Segmentation fault (11) [localhost:05692] Signal code: Address not mapped (1) [localhost:05692] Failing at address: 0x19 [localhost:05684] *** Process received signal *** [localhost:05684] Signal: Segmentation fault (11) [localhost:05684] Signal code: Address not mapped (1) [localhost:05684] Failing at address: 0x19 [localhost:05674] *** Process received signal *** [localhost:05674] Signal: Segmentation fault (11) [localhost:05674] Signal code: Address not mapped (1) [localhost:05674] Failing at address: 0x19 [localhost:05684] [ 0] /lib64/tls/libpthread.so.0 [0x314a80c4f0] [localhost:05684] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x3149d69365] [localhost:05684] [ 2] openmx [0x6ea9f1] [localhost:05684] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6df005] [localhost:05684] [ 4] openmx(main+0xddc) [0x42fb94] [localhost:05684] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3149d1c3fb] [localhost:05684] [ 6] openmx [0x42ed2a] [localhost:05684] *** End of error message *** [localhost:05691] [ 0] /lib64/tls/libpthread.so.0 [0x314a80c4f0] [localhost:05691] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x3149d69365] [localhost:05691] [ 2] openmx [0x6ea9f1] [localhost:05691] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6df005] [localhost:05691] [ 4] openmx(main+0xddc) [0x42fb94] [localhost:05691] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3149d1c3fb] [localhost:05691] [ 6] openmx [0x42ed2a] [localhost:05691] *** End of error message *** -------------------------------------------------------------------------- mpirun noticed that process rank 1 with PID 5675 on node localhost.localdomain exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- 3 total processes killed (some possibly by mpirun during cleanup) I need your help at this stage to know how and why does it appear even if it is giving correct result. Your suggestions may be helpful to us. Thank you.

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Re: Incomplete NEGF run with correct transmission vs energy result ( No.1 ) Date: 2016/07/21 19:14 Name: Artem Pulkin You have all the information you need: [localhost:05691] [ 0] /lib64/tls/libpthread.so.0 [0x314a80c4f0] [localhost:05691] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x3149d69365] [localhost:05691] [ 2] openmx [0x6ea9f1] [localhost:05691] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6df005] [localhost:05691] [ 4] openmx(main+0xddc) [0x42fb94] [localhost:05691] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3149d1c3fb] [localhost:05691] [ 6] openmx [0x42ed2a] Provided you compiled with debugging symbols (-g) run addr2line -e /your/path/to/openmx 0x6ea9f1 0x6df005 0x42fb94 0x42ed2a and check which lines fail. It will likely be an assignemnt to an array. Re: Incomplete NEGF run with correct transmission vs energy result ( No.2 ) Date: 2016/07/24 17:57 Name: Vipin Kumar Dear sir, I am optimizing my geometry using DIIS optimization. My system contains 289 atoms. When I am looking at *.DFTSCF file, it is showing the following result: *********************************************************** *********************************************************** SCF history at MD= 1 *********************************************************** *********************************************************** SCF= 1 NormRD= 1.000000000000 Uele= -2324271970357.147949218750 SCF= 2 NormRD= 18.851511589123 Uele= -2324271970363.424316406250 SCF= 3 NormRD= 18.529418178350 Uele= -2324271970362.662109375000 SCF= 4 NormRD= 13.887966533865 Uele= -2324271970356.577636718750 SCF= 5 NormRD= 11.083859712264 Uele= -2324271970350.618652343750 My question is that why the values in the last column are too negatively high. Does it depend on the size of the system (large or small), I mean number of atoms. I am in doubt by looking this much value in the last column. Can you please explain me the actual reason that why am I getting this much value. My input file is: # # File Name # System.CurrrentDirectory ./ # default=./ System.Name LBNR_DIIS level.of.stdout 1 # default=1 (1-3) level.of.fileout 0 # default=1 (0-2) # # Definition of Atomic Species # Species.Number 2 <Definition.of.Atomic.Species B B7.0-s2p2d1 B_PBE13 H H5.0-s2 H_PBE13 Definition.of.Atomic.Species> # # Atoms # Atoms.Number 289 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 B 0.000000 0.000000 0.000000 1.500000 1.500000 2 B 0.000000 1.675000 0.000000 1.500000 1.500000 3 B 0.000000 0.837500 -1.450593 1.500000 1.500000 4 B 0.000000 -0.837500 -1.450593 1.500000 1.500000 5 B 0.000000 2.512500 -1.450593 1.500000 1.500000 6 B 0.000000 4.187500 -1.450593 1.500000 1.500000 ...... ...... ...... 281 B 0.000000 19.262500 30.46244 1.500000 1.500000 282 H 0.000000 -2.028500 24.66007 0.500000 0.500000 283 H 0.000000 -1.191000 26.11067 0.500000 0.500000 284 H 0.000000 -1.191000 29.01185 0.500000 0.500000 285 H 0.000000 -2.028500 30.46244 0.500000 0.500000 286 H 0.000000 20.453500 24.66007 0.500000 0.500000 287 H 0.000000 19.616000 26.11067 0.500000 0.500000 288 H 0.000000 19.616000 29.01185 0.500000 0.500000 289 H 0.000000 20.453500 30.46244 0.500000 0.500000 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 0.000000 0.000000 41.913033 10.000000 0.000000 0.000000 0.000000 32.482000 0.000000 Atoms.UnitVectors> # # SCF or Electronic System # scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 300.0 # default=300 (K) scf.energycutoff 300.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver band # DC|GDC|Cluster|Band scf.Kgrid 11 1 1 # means n1 x n2 x n3 scf.Mixing.Type Rmm-Diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.10 # default=0.30 scf.Min.Mixing.Weight 0.01 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Mixing.History 14 # default=5 scf.Mixing.StartPulay 7 # default=6 scf.criterion 1.0e-7 # default=1.0e-6 (Hartree) # # MD or Geometry Optimization # MD.Type DIIS # Nomd|Opt|NVE|NVT_VS|NVT_NH MD.Opt.DIIS.History 3 # default=3 MD.Opt.StartDIIS 7 # default=5 MD.maxIter 200 # default=1 MD.Opt.criterion 1.0e-4 # default=1.0e-4 (Hartree/bohr) Re: Incomplete NEGF run with correct transmission vs energy result ( No.3 ) Date: 2016/07/26 19:42 Name: Artem Pulkin You did not specify the unit cell.

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