Error with the NEGF Calculation |
- Date: 2025/04/05 12:35
- Name: Kieran
<masrfa@googlemail.com>
- Dear All,
I submitted the NEGF calculation for the graphene system.
Here is the input file.
==================================================================================================
# File Name
System.CurrrentDirectory ./ # default=./
System.Name negf-graphene
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-graphene.hks
NEGF.filename.hks.r lead-graphene.hks
NEGF.Num.Poles 100 # default=150
NEGF.scf.Kgrid 1 1 # default=1 1
NEGF.SCF.Iter.Band 50
NEGF.bias.voltage 0.01 # 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 -10.14849932893 9.85150067107 5.0e-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 3 # default=1
<NEGF.Channel.energy
-0.64849932893
-0.14849932893
0.35150067107
NEGF.Channel.energy> # default 0.0
NEGF.Channel.Num 3 # defualt=5(for collinear), 10(for Non-collinear)
# Definition of Atomic Species
Species.Number 1
<Definition.of.Atomic.Species
C C6.0-s2p2d1 C_PBE19
Definition.of.Atomic.Species>
# Atoms
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 8
<Atoms.SpeciesAndCoordinates
1 C 25.56468 0.00000 10.00000 2.0 2.0
2 C 27.69507 1.23000 10.00000 2.0 2.0
3 C 26.27481 1.23000 10.00000 2.0 2.0
4 C 28.4052 0.00000 10.00000 2.0 2.0
5 C 29.82546 0.00000 10.00000 2.0 2.0
6 C 31.95585 1.23000 10.00000 2.0 2.0
7 C 30.53559 1.23000 10.00000 2.0 2.0
8 C 32.66598 0.00000 10.00000 2.0 2.0
Atoms.SpeciesAndCoordinates>
# Lead-Left
LeftLeadAtoms.Number 24
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.00000 0.00000 10.00000 2.0 2.0
2 C 2.13039 1.23000 10.00000 2.0 2.0
3 C 0.71013 1.23000 10.00000 2.0 2.0
4 C 2.84052 0.00000 10.00000 2.0 2.0
5 C 4.26078 0.00000 10.00000 2.0 2.0
6 C 6.39117 1.23000 10.00000 2.0 2.0
7 C 4.97091 1.23000 10.00000 2.0 2.0
8 C 7.10130 0.00000 10.00000 2.0 2.0
9 C 8.52156 0.00000 10.00000 2.0 2.0
10 C 10.65195 1.23000 10.00000 2.0 2.0
11 C 9.231690 1.23000 10.00000 2.0 2.0
12 C 11.36208 0.00000 10.00000 2.0 2.0
13 C 12.78234 0.00000 10.00000 2.0 2.0
14 C 14.91273 1.23000 10.00000 2.0 2.0
15 C 13.49247 1.23000 10.00000 2.0 2.0
16 C 15.62286 0.00000 10.00000 2.0 2.0
17 C 17.04312 0.00000 10.00000 2.0 2.0
18 C 19.17351 1.23000 10.00000 2.0 2.0
19 C 17.75325 1.23000 10.00000 2.0 2.0
20 C 19.88364 0.00000 10.00000 2.0 2.0
21 C 21.30390 0.00000 10.00000 2.0 2.0
22 C 23.43429 1.23000 10.00000 2.0 2.0
23 C 22.01403 1.23000 10.00000 2.0 2.0
24 C 24.14442 0.00000 10.00000 2.0 2.0
LeftLeadAtoms.SpeciesAndCoordinates>
# Lead-Right
RightLeadAtoms.Number 24
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 34.08624 0.00000 10.00000 2.0 2.0
2 C 36.21663 1.23000 10.00000 2.0 2.0
3 C 34.79637 1.23000 10.00000 2.0 2.0
4 C 36.92676 0.00000 10.00000 2.0 2.0
5 C 38.34702 0.00000 10.00000 2.0 2.0
6 C 40.47741 1.23000 10.00000 2.0 2.0
7 C 39.05715 1.23000 10.00000 2.0 2.0
8 C 41.18754 0.00000 10.00000 2.0 2.0
9 C 42.6078 0.00000 10.00000 2.0 2.0
10 C 44.73819 1.23000 10.00000 2.0 2.0
11 C 43.31793 1.23000 10.00000 2.0 2.0
12 C 45.44832 0.00000 10.00000 2.0 2.0
13 C 46.86858 0.00000 10.00000 2.0 2.0
14 C 48.99897 1.23000 10.00000 2.0 2.0
15 C 47.57871 1.23000 10.00000 2.0 2.0
16 C 49.7091 0.00000 10.00000 2.0 2.0
17 C 51.12936 0.00000 10.00000 2.0 2.0
18 C 53.25975 1.23000 10.00000 2.0 2.0
19 C 51.83949 1.23000 10.00000 2.0 2.0
20 C 53.96988 0.00000 10.00000 2.0 2.0
21 C 55.39014 0.00000 10.00000 2.0 2.0
22 C 57.52053 1.23000 10.00000 2.0 2.0
23 C 56.10027 1.23000 10.00000 2.0 2.0
24 C 58.23066 0.00000 10.00000 2.0 2.0
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 10 103 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.010 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.020 # default=0.40
scf.Mixing.History 20 # default=5
scf.Mixing.StartPulay 7 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
scf.Kerker.factor 30.0 # default=1
NEGF.Poisson.Solver FFT
==================================================================================================
The calculation failed with the following error message.
******************* MD= 1 SCF= 1 *******************
<TRAN_Set_Electrode_Grid>
<TRAN_Allocate_Lead_Region>
<TRAN_Allocate_Cregion: NUM_c=728 NUM_e=312 312>
<TRAN_Add_Density_Lead>
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 3792 RUNNING AT fb0802
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
Intel(R) MPI Library troubleshooting guide:
https://software.intel.com/node/561764
===================================================================================
This is my shell script for submitting the job.
==================================================================================================
#!/bin/bash
#SBATCH -N 1
#SBATCH -p vip_17
#SBATCH -n 64
module load openmx/3.9
mpirun -np 2 openmx NEGF-graphene.dat
==================================================================================================
Would anyone please tell me why the calculation failed? What is the problem with my input file?
Thank you in advance.
Kieran
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