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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