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Aborted in the NEGF calculation with OpenMX
Date: 2024/06/18 18:29
Name: Kieran   <skn_neu@hotmail.co.uk>

Dear All,

I am running the NEGF calculation with OpenMX. Here is the input file.
# File Name
System.CurrrentDirectory        ./    # default=./
System.Name                      negf-al2o3grapheneal2o3
level.of.stdout                  1    # default=1 (1-3)
level.of.fileout                  0    # default=1 (0-2)
DATA.PATH                        /public21/soft/openmx/openmx3.9/DFT_DATA19/


NEGF.filename.hks.l    lead-Al2O3.hks
NEGF.filename.hks.r    lead-Al2O3.hks

NEGF.Num.Poles            100      # default=150
NEGF.scf.Kgrid            1 1      # default=1 1
NEGF.SCF.Iter.Band          50

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    -15.0 25.0 5.0e-3  #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div        100      # default=200
NEGF.Dos.Kgrid            1 1      # default=1 1

# Transmission & Eigen Channel
NEGF.tran.Analysis        on        #  default on
NEGF.tran.energydiv        100      # default=200
NEGF.tran.energyrange -10 10 1.0e-3  # default=-10.0 10.0 1.0e-3 (eV)
NEGF.tran.Kgrid            1 1      # default= 1 1
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        5        # default=1
<NEGF.Channel.energy
0.29558808127827
0.04558808127827
-0.20441191872173
-0.45441191872173
-0.70441191872173
NEGF.Channel.energy>                # default 0.0
NEGF.Channel.Num            5        # defualt=5(for collinear), 10(for Non-collinear)

# Definition of Atomic Species
Species.Number              4
<Definition.of.Atomic.Species
O  O6.0-s2p2d1  O_PBE19
Al Al7.0-s2p2d1 Al_PBE19
C  C6.0-s2p2d1  C_PBE19
H  H6.0-s2p1    H_PBE19
Definition.of.Atomic.Species>

# Atoms
Atoms.SpeciesAndCoordinates.Unit  Ang # Ang|AU
Atoms.Number        628
<Atoms.SpeciesAndCoordinates
          1 O  0.0000000000000000        1.4562538860000001        48.473975936124418        2.00000000      4.00000000   
          2 O  4.1213998790000002        3.8357539180000000        48.473975936124418        2.00000000      4.00000000
......
......
......
        627 H  5.4952273370000002        8.0867776869999997        63.967111388213773        1.00000000      0.00000000   
        628 H  5.4952273370000002        8.0867776869999997        65.711890975213777        1.00000000      0.00000000
Atoms.SpeciesAndCoordinates>

# Lead-Left
LeftLeadAtoms.Number        240
<LeftLeadAtoms.SpeciesAndCoordinates          # Unit=Ang.
          1 O  0.0000000000000000        1.4562538860000001        22.491727829137208        2.00000000      4.00000000   
          2 O  4.1213998790000002        3.8357539180000000        22.491727829137208        2.00000000      4.00000000
......
......
......
        239 Al  2.7475724220000002        4.7589998250000001        6.0103421209999999        2.00000000      1.00000000   
        240 Al  6.8689723010000003        7.1384997370000001        6.0103421209999999        2.00000000      1.00000000
LeftLeadAtoms.SpeciesAndCoordinates>

# Lead-Right
RightLeadAtoms.Number        240
<RightLeadAtoms.SpeciesAndCoordinates          # Unit=Ang.
          1 O  0.0000000000000000        1.4562538860000001        118.63821943473818        2.00000000      4.00000000   
          2 O  4.1213998790000002        3.8357539180000000        118.63821943473818        2.00000000      4.00000000
......
......
......
        239 Al  2.7475724220000002        4.7589998250000001        102.15683372660096        2.00000000      1.00000000   
        240 Al  6.8689723010000003        7.1384997370000001        102.15683372660096        2.00000000      1.00000000
RightLeadAtoms.SpeciesAndCoordinates>

# SCF or Electronic System
scf.XcType                  LDA        # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization        off        # On|Off|NC
scf.ElectronicTemperature  600.0      # default=300 (K)
scf.energycutoff          350.0      # default=150 (Ry)
scf.maxIter                100        # default=40
scf.EigenvalueSolver      NEGF        # DC|GDC|Cluster|Band
#scf.lapack.dste            dstevx      # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid                  100 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      0.020      # default=0.30
scf.Min.Mixing.Weight      0.020      # default=0.001
scf.Max.Mixing.Weight      0.050      # default=0.40
scf.Mixing.History          100        # default=5
scf.Mixing.StartPulay      20        # default=6
scf.criterion            1.0e-7      # default=1.0e-6 (Hartree)
scf.Kerker.factor          30.0        # default=1
NEGF.Poisson.Solver      FFT

After I launched the calculation, I received the following error message.

The number of threads in each node for OpenMP parallelization is 1.


*******************************************************
*******************************************************
Welcome to OpenMX  Ver. 3.9                         
Copyright (C), 2002-2019, T. Ozaki                   
OpenMX comes with ABSOLUTELY NO WARRANTY.           
This is free software, and you are welcome to       
redistribute it under the constitution of the GNU-GPL.
*******************************************************
*******************************************************


***********************************************************
***********************************************************
Welcome to the NEGF extension
The prototype fortran code: by Hisashi Kondo.
The current version: by Hiori Kino and Taisuke Ozaki.
***********************************************************
***********************************************************



<TRAN_RestartFile called, mode=read pos=left>
<TRAN_Input_HKS>
<TRAN_RestartFile called, mode=read pos=right>
<TRAN_Input_HKS>

Intrinsic chemical potential (eV) of the leads
  Left lead:  -5.562331316720
  Right lead: -5.562331316720
  add voltage =  0.0000 (eV) to the  left lead: new ChemP (eV):  -5.5623
  add voltage =  0.0000 (eV) to the right lead: new ChemP (eV):  -5.5623

Parameters for the integration of the non-equilibrium part
  lower bound:          -5.562331316720 (eV)
  upper bound:          -5.562331316720 (eV)
  energy step:            0.020000000000 (eV)
  number of steps:            0   
  Warning: the energy step you specified is larger than the integration range.


<Input_std>  Your input file was normally read.
<Input_std>  The system includes 4 species and 1108 atoms.

*******************************************************
                    PAO and VPS                     
*******************************************************

<SetPara_DFT>  PAOs of species O were normally found.
<SetPara_DFT>  PAOs of species Al were normally found.
<SetPara_DFT>  PAOs of species C were normally found.
<SetPara_DFT>  PAOs of species H were normally found.
<SetPara_DFT>  VPSs of species O were normally found.
              O_PBE19.vps is j-dependent.
              In case of scf.SpinOrbit.Coupling=off,
              j-dependent pseudo potentials are averaged by j-degeneracy,
              which corresponds to a scalar relativistic treatment.
<SetPara_DFT>  VPSs of species Al were normally found.
              Al_PBE19.vps is j-dependent.
              In case of scf.SpinOrbit.Coupling=off,
              j-dependent pseudo potentials are averaged by j-degeneracy,
              which corresponds to a scalar relativistic treatment.
<SetPara_DFT>  VPSs of species C were normally found.
              C_PBE19.vps is j-dependent.
              In case of scf.SpinOrbit.Coupling=off,
              j-dependent pseudo potentials are averaged by j-degeneracy,
              which corresponds to a scalar relativistic treatment.
<SetPara_DFT>  VPSs of species H were normally found.
              H_PBE19.vps is j-dependent.
              In case of scf.SpinOrbit.Coupling=off,
              j-dependent pseudo potentials are averaged by j-degeneracy,
              which corresponds to a scalar relativistic treatment.

*******************************************************
    Fourier transform of PAO and projectors of VNL   
*******************************************************

<FT_PAO>          Fourier transform of pseudo atomic orbitals
<FT_NLP>          Fourier transform of non-local projectors
<FT_ProExpn_VNA>  Fourier transform of VNA separable projectors
<FT_VNA>          Fourier transform of VNA potentials
<FT_ProductPAO>  Fourier transform of product of PAOs

*******************************************************
  Allocation of atoms to proccesors at MD_iter=    1   
*******************************************************

proc =  0  # of atoms=  8  estimated weight=        8.00000
proc =  1  # of atoms=  9  estimated weight=        9.00000
proc =  2  # of atoms=  8  estimated weight=        8.00000
......
......
......
Atom967=  3 Atom968=  3 Atom969=  3 Atom970=  3 Atom971=  3 Atom972=  3 Atom973=  3
Atom974=  3 Atom975=  3 Atom976=  3 Atom977=  3 Atom978=  3 Atom979=  3 Atom980=  3
Atom981=  3 Atom982=  3 Atom983=  3 Atom984=  3 Atom985=  3 Atom986=  3 Atom987=  3
Atom988=  3 Atom989=  3 Atom990=  3 Atom991=  3 Atom992=  3 Atom993=  3 Atom994=  3
Atom995=  3 Atom996=  3 Atom997=  3 Atom998=  3 Atom999=  3

===================================================================================
=  BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=  PID 59293 RUNNING AT fb0802
=  EXIT CODE: 9
=  CLEANING UP REMAINING PROCESSES
=  YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
  Intel(R) MPI Library troubleshooting guide:
      https://software.intel.com/node/561764
===================================================================================

Is it because of the memory issue or something else? Would anyone please give me some suggestions on the solution?

Thank you in advance.
e
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