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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.
e
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