Segmetation fault |
- Date: 2024/05/11 17:27
- Name: Kieran
<skn_neu@hotmail.co.uk>
- Dear All,
I used the following input file to do the NEGF calculation.
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 /THL8/home/kns/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 0.1 # 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
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
-4.679946762
-4.929946762
-5.179946762
-5.429946762
-5.679946762
NEGF.Channel.energy> # default 0.0
NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear)
Species.Number 3
<Definition.of.Atomic.Species
O O6.0-s2p2d1 O_PBE19
Al Al7.0-s2p2d1 Al_PBE19
C C6.0-s2p2d1 C_PBE19
Definition.of.Atomic.Species>
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 76
<Atoms.SpeciesAndCoordinates
1 O -0.72812694300000003 1.2611528640000000 22.491650581500000 2.0 4.0
......
......
......
76 C 1.1897739169999999 3.4344983099999999 28.497048378500001 2.0 2.0
Atoms.SpeciesAndCoordinates>
LeftLeadAtoms.Number 30
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 O 1.4562538860000001 0.0000000000000000 3.0052503646729889 2.0 4.0
......
......
......
30 Al 0.0000000000000000 2.7476098539999998 6.4954992826729887 2.0 1.0
LeftLeadAtoms.SpeciesAndCoordinates>
RightLeadAtoms.Number 30
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 O 1.4562538860000001 0.0000000000000000 45.993250280772990 2.0 4.0
......
......
......
30 Al 0.0000000000000000 2.7476098539999998 49.483499198772989 2.0 1.0
RightLeadAtoms.SpeciesAndCoordinates>
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.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 submitted the calculation, I obtained the segmentation fault as follows.
*******************************************************
The extended cell consists of Left0-Center-Right0.
The cells of left and right reads are connected as.
...|Left2|Left1|Left0-Center-Right0|Right1|Right2...
Each atom in the extended cell is assigned as follows:
where '12' and '2' mean that they are in 'Left0', and
'12' has overlap with atoms in the Left1,
and '13' and '3' mean that they are in 'Right0', and
'13' has overlap with atoms in the 'Right1', and also
'1' means atom in the 'Center'.
********************************************************
Atom1 = 12 Atom2 = 2 Atom3 = 12 Atom4 = 2 Atom5 = 12 Atom6 = 2 Atom7 = 2
Atom8 = 12 Atom9 = 2 Atom10 = 12 Atom11 = 2 Atom12 = 12 Atom13 = 2 Atom14 = 2
Atom15 = 2 Atom16 = 12 Atom17 = 2 Atom18 = 12 Atom19 = 12 Atom20 = 2 Atom21 = 12
Atom22 = 2 Atom23 = 2 Atom24 = 2 Atom25 = 12 Atom26 = 12 Atom27 = 12 Atom28 = 12
Atom29 = 2 Atom30 = 2 Atom31 = 1 Atom32 = 1 Atom33 = 1 Atom34 = 1 Atom35 = 1
Atom36 = 1 Atom37 = 1 Atom38 = 1 Atom39 = 1 Atom40 = 1 Atom41 = 1 Atom42 = 1
Atom43 = 1 Atom44 = 1 Atom45 = 1 Atom46 = 1 Atom47 = 1 Atom48 = 1 Atom49 = 1
Atom50 = 1 Atom51 = 1 Atom52 = 1 Atom53 = 1 Atom54 = 1 Atom55 = 1 Atom56 = 1
Atom57 = 1 Atom58 = 1 Atom59 = 1 Atom60 = 1 Atom61 = 1 Atom62 = 1 Atom63 = 1
Atom64 = 1 Atom65 = 1 Atom66 = 1 Atom67 = 1 Atom68 = 1 Atom69 = 1 Atom70 = 1
Atom71 = 1 Atom72 = 1 Atom73 = 1 Atom74 = 1 Atom75 = 1 Atom76 = 1 Atom77 = 1
Atom78 = 1 Atom79 = 1 Atom80 = 1 Atom81 = 1 Atom82 = 1 Atom83 = 1 Atom84 = 1
Atom85 = 1 Atom86 = 1 Atom87 = 1 Atom88 = 1 Atom89 = 1 Atom90 = 1 Atom91 = 1
Atom92 = 1 Atom93 = 1 Atom94 = 1 Atom95 = 1 Atom96 = 1 Atom97 = 1 Atom98 = 1
Atom99 = 1 Atom100= 1 Atom101= 1 Atom102= 1 Atom103= 1 Atom104= 1 Atom105= 1
Atom106= 1 Atom107= 3 Atom108= 13 Atom109= 3 Atom110= 13 Atom111= 3 Atom112= 13
Atom113= 3 Atom114= 3 Atom115= 13 Atom116= 3 Atom117= 13 Atom118= 3 Atom119= 13
Atom120= 3 Atom121= 13 Atom122= 3 Atom123= 13 Atom124= 3 Atom125= 3 Atom126= 13
Atom127= 3 Atom128= 13 Atom129= 13 Atom130= 13 Atom131= 3 Atom132= 3 Atom133= 3
Atom134= 3 Atom135= 13 Atom136= 13
*******************************************************
SCF calculation at MD = 1
*******************************************************
<MD= 1> Calculation of the overlap matrix
<MD= 1> Calculation of the nonlocal matrix
<MD= 1> Calculation of the VNA projector matrix
******************* MD= 1 SCF= 1 *******************
<TRAN_Set_Electrode_Grid>
<TRAN_Allocate_Lead_Region>
<TRAN_Allocate_Cregion: NUM_c=1768 NUM_e=390 390>
<TRAN_Add_Density_Lead>
yhrun: error: cn1476: task 167: Segmentation fault
yhrun: error: cn1474: tasks 90-92: Segmentation fault
yhrun: error: cn1471: tasks 2,6-9,11,17,22: Segmentation fault
yhrun: error: cn1475: tasks 115,122,132: Segmentation fault
yhrun: error: cn1472: task 28: Segmentation fault
yhrun: error: cn1476: tasks 147,149,156: Segmentation fault
yhrun: error: cn1473: tasks 57,61,63,66,69-71,77: Segmentation fault
yhrun: error: cn1475: tasks 112,114,116,121,124-125,127-128,130-131,136,138-139: Segmentation fault
yhrun: error: cn1471: tasks 0-1,3-5,10,13-16,18-20,23-27: Segmentation fault
yhrun: error: cn1474: tasks 86-88,93-94,99-100,102,106-108,110-111: Segmentation fault
yhrun: error: cn1472: tasks 29-35,38-39,41-55: Segmentation fault
yhrun: error: cn1476: tasks 140-146,148,150-155,157,159-166: Segmentation fault
yhrun: error: cn1473: tasks 58-60,62,64-65,67-68,72-76,78-83: Segmentation fault
yhrun: error: cn1476: task 158: Segmentation fault
yhrun: error: cn1472: task 37: Segmentation fault
yhrun: error: cn1474: tasks 84-85,89,95-98,101,103-105,109: Segmentation fault
yhrun: error: cn1475: tasks 113,117-120,123,126,129,133-135,137: Segmentation fault
yhrun: error: cn1471: task 21: Segmentation fault
yhrun: error: cn1473: task 56: Segmentation fault
yhrun: error: cn1472: task 40: Segmentation fault
yhrun: error: cn1472: task 36: Segmentation fault
yhrun: error: cn1471: task 12: Segmentation fault
Would anyone please tell me what is wrong with my parameter settings?
Thank you in advance.
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