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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.
メンテ
Page: [1]

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.
メンテ
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)
メンテ
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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