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.
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