OpenMX program automatically exit |
- Date: 2014/05/12 12:01
- Name: chow
<chowwh2012@gmail.com>
- Dear allF
I have already caculated Lead, file"au108.hks" and "au108-r.hks" generated.
When I performed NEGF calculate on CentOS, OpenMX program automatically exit like that:
[root@localhost Co-NEGF]# (mpirun -np 8 openmx NEGF-Co3au108.dat>NEGF-Co3au108.std &)
[root@localhost Co-NEGF]#
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 28596 on node localhost.localdomain exited on signal 9 (Killed).
--------------------------------------------------------------------------
file std end with the following data:
*******************************************************
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=12516 NUM_e=3888 3888>
<TRAN_Add_Density_Lead>
<TRAN_Add_ADensity_Lead>
<TRAN_Poisson_FFT> Solving Poisson's equation...
<NEGF> Solving the eigenvalue problem...
KGrids1: 0.00000
KGrids2: 0.00000
KGrids3: 0.00000
and fie Ucell:
***********************************************************
***********************************************************
Required cutoff energy (Ryd) for 3D-grids = 250.0000
Used cutoff energy (Ryd) for 3D-grids = 251.9893, 255.2399, 255.2398
Num. of grids of a-, b-, and c-axes = 324, 144, 144
Num.Grid1. 324
Num.Grid2. 144
Num.Grid3. 144
Cell_Volume = 59367.630604446334 (Bohr^3)
GridVol = 0.008836488609 (Bohr^3)
Cell vectors (bohr) of the grid cell (gtv)
gtv_a = 0.000000000000, -0.000000000000, 0.197905935203
gtv_b = 0.227062388315, 0.000000000000, 0.000000000000
gtv_c = -0.113531456620, 0.196641736828, 0.000000000000
|gtv_a| = 0.197905935203
|gtv_b| = 0.227062388315
|gtv_c| = 0.227062467847
***********************************************************
***********************************************************
My input file:
#
# File Name
#
System.CurrrentDirectory ./ # default=./
DATA.PATH /opt/openmx3.7/DFT_DATA13/ # default=../DFT_DATA
System.Name Co3au108
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
NEGF.filename.hks.l au108.hks
NEGF.filename.hks.r au108-r.hks
NEGF.Poisson.Solver FFT # FD|FFT, default=FD
NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1
NEGF.scf.Iter.Band 6 # defalut=6
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 -20.0 20.0 1.0e-4 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 4000 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1
NEGF.tran.energydiv 800 # default=200
NEGF.tran.energyrange -4 4 0.001 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 3 3 # default= 1 1
#
# Definition of Atomic Species
#
Species.Number 6
<Definition.of.Atomic.Species
Au Au7.0-s2p2d2 Au_PBE13
C C5.0-s2p2d1 C_CA13
H H5.0-s2p2 H_CA13
N N5.0-s2p2d1 N_CA13
S S7.0-s2p2d2 S_CA13
Co Co6.0H-s2p2d2 Co_PBE13H
Definition.of.Atomic.Species>
LeftLeadAtoms.Number 108
<LeftLeadAtoms.SpeciesAndCoordinates
1 Au 0.00000000 0.00000000 1.17724684 8.50 8.50
2 Au 2.88375823 0.00000000 1.17724684 8.50 8.50
....Au atoms
108 Au 7.20939558 14.15197802 5.88640431 8.50 8.50
LeftLeadAtoms.SpeciesAndCoordinates>
RightLeadAtoms.Number 108
<RightLeadAtoms.SpeciesAndCoordinates
1 Au 0.00000000 1.66493859 28.04516178 8.50 8.50
.....Au atoms
108 Au 7.20939558 12.48703943 32.75431925 8.50 8.50
RightLeadAtoms.SpeciesAndCoordinates>
#<RightLeadAtoms.UnitVectors
Atoms.Number 165
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Au 0.00000000 0.00000000 8.24098304 8.50 8.50
...... Au atoms
36 Au 7.20939558 12.48703943 8.24098304 8.50 8.50
37 S 2.88375823 6.65975436 9.95098304 3.00 3.00
38 C 2.88375823 6.65975436 11.49358304 2.00 2.00
39 N 2.88375823 6.65975436 12.60088304 2.50 2.50
40 H 1.21255823 4.85975436 13.03398304 0.50 0.50
41 H 4.68375823 4.98855436 13.03398304 0.50 0.50
42 H 1.08375823 8.33095436 13.03398304 0.50 0.50
43 H 4.55495823 8.45975436 13.03398304 0.50 0.50
44 H 0.24305823 2.78575436 13.14688304 0.50 0.50
45 H 6.75775823 4.01905436 13.14688304 0.50 0.50
46 H -0.99024177 9.30045436 13.14688304 0.50 0.50
47 H 5.52445823 10.53375436 13.14688304 0.50 0.50
48 C 1.33355823 4.34365436 13.80868304 2.00 2.00
49 C 5.19985823 5.10955436 13.80868304 2.00 2.00
50 C 0.56765823 8.20995436 13.80868304 2.00 2.00
51 C 4.43395823 8.97585436 13.80868304 2.00 2.00
52 C 0.74175823 3.11345436 13.86878304 2.00 2.00
53 C 6.43005823 4.51775436 13.86878304 2.00 2.00
54 C -0.66254177 8.80175436 13.86878304 2.00 2.00
55 C 5.02575823 10.20605436 13.86878304 2.00 2.00
56 Co 2.88375823 6.65975436 14.65048304 9.00 8.00
57 N 2.08415823 4.85715436 14.80828304 2.50 2.50
58 N 4.68635823 5.86015436 14.80828304 2.50 2.50
59 N 1.08115823 7.45935436 14.80828304 2.50 2.50
60 N 3.68335823 8.46235436 14.80828304 2.50 2.50
61 C 0.89475823 2.36015436 15.01738304 2.00 2.00
62 C 7.18335823 4.67075436 15.01738304 2.00 2.00
63 C -1.41584177 8.64875436 15.01738304 2.00 2.00
64 C 4.87275823 10.95935436 15.01738304 2.00 2.00
65 H 0.49385823 1.51345436 15.08418304 0.50 0.50
66 H 8.03005823 4.26985436 15.08418304 0.50 0.50
67 H -2.26254177 9.04965436 15.08418304 0.50 0.50
68 H 5.27365823 11.80605436 15.08418304 0.50 0.50
69 C 2.23245823 4.12475436 15.94808304 2.00 2.00
70 C 5.41875823 6.00845436 15.94808304 2.00 2.00
71 C 0.34875823 7.31105436 15.94808304 2.00 2.00
72 C 3.53505823 9.19475436 15.94808304 2.00 2.00
73 C 1.63255823 2.85785436 16.05188304 2.00 2.00
74 C 6.68565823 5.40855436 16.05188304 2.00 2.00
75 C -0.91814177 7.91095436 16.05188304 2.00 2.00
76 C 4.13495823 10.46165436 16.05188304 2.00 2.00
77 H 1.73935823 2.35315436 16.83388304 0.50 0.50
78 H 7.19035823 5.51535436 16.83388304 0.50 0.50
79 H -1.42284177 7.80415436 16.83388304 0.50 0.50
80 H 4.02815823 10.96635436 16.83388304 0.50 0.50
81 N 2.88375823 4.76435436 16.96578304 2.50 2.50
82 N 0.98835823 6.65975436 16.96578304 2.50 2.50
83 Co 2.88375823 6.65975436 16.96578304 8.00 9.00
84 N 4.77915823 6.65975436 16.96578304 2.50 2.50
85 N 2.88375823 8.55515436 16.96578304 2.50 2.50
86 H 4.02815823 2.35315436 17.09768304 0.50 0.50
87 H -1.42284177 5.51535436 17.09768304 0.50 0.50
88 H 7.19035823 7.80415436 17.09768304 0.50 0.50
89 H 1.73935823 10.96635436 17.09768304 0.50 0.50
90 C 4.13495823 2.85785436 17.87968304 2.00 2.00
91 C -0.91814177 5.40855436 17.87968304 2.00 2.00
92 C 6.68565823 7.91095436 17.87968304 2.00 2.00
93 C 1.63255823 10.46165436 17.87968304 2.00 2.00
94 C 3.53505823 4.12475436 17.98348304 2.00 2.00
95 C 0.34875823 6.00845436 17.98348304 2.00 2.00
96 C 5.41875823 7.31105436 17.98348304 2.00 2.00
97 C 2.23245823 9.19475436 17.98348304 2.00 2.00
98 H 5.27365823 1.51345436 18.84738304 0.50 0.50
99 H -2.26254177 4.26985436 18.84738304 0.50 0.50
100 H 8.03005823 9.04965436 18.84738304 0.50 0.50
101 H 0.49385823 11.80605436 18.84738304 0.50 0.50
102 C 4.87275823 2.36015436 18.91418304 2.00 2.00
103 C -1.41584177 4.67075436 18.91418304 2.00 2.00
104 C 7.18335823 8.64875436 18.91418304 2.00 2.00
105 C 0.89475823 10.95935436 18.91418304 2.00 2.00
106 N 3.68335823 4.85715436 19.12328304 2.50 2.50
107 N 1.08115823 5.86015436 19.12328304 2.50 2.50
108 N 4.68635823 7.45935436 19.12328304 2.50 2.50
109 N 2.08415823 8.46235436 19.12328304 2.50 2.50
110 Co 2.88375823 6.65975436 19.28108304 9.00 8.00
111 C 5.02575823 3.11345436 20.06278304 2.00 2.00
112 C -0.66254177 4.51775436 20.06278304 2.00 2.00
113 C 6.43005823 8.80175436 20.06278304 2.00 2.00
114 C 0.74175823 10.20605436 20.06278304 2.00 2.00
115 C 4.43395823 4.34365436 20.12288304 2.00 2.00
116 C 0.56765823 5.10955436 20.12288304 2.00 2.00
117 C 5.19985823 8.20995436 20.12288304 2.00 2.00
118 C 1.33355823 8.97585436 20.12288304 2.00 2.00
119 H 5.52445823 2.78575436 20.78468304 0.50 0.50
120 H -0.99024177 4.01905436 20.78468304 0.50 0.50
121 H 6.75775823 9.30045436 20.78468304 0.50 0.50
122 H 0.24305823 10.53375436 20.78468304 0.50 0.50
123 H 4.55495823 4.85975436 20.89758304 0.50 0.50
124 H 1.08375823 4.98855436 20.89758304 0.50 0.50
125 H 4.68375823 8.33095436 20.89758304 0.50 0.50
126 H 1.21255823 8.45975436 20.89758304 0.50 0.50
127 N 2.88375823 6.65975436 21.33068304 2.50 2.50
128 C 2.88375823 6.65975436 22.43798304 2.00 2.00
129 S 2.88375823 6.65975436 23.98058304 3.00 3.00
130 Au 0.00000000 0.00000000 25.69058304 8.50 8.50
...... Au atoms
165 Au 7.20939558 12.48703943 25.69058304 8.50 8.50
Atoms.SpeciesAndCoordinates>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization NC # On|Off|NC
scf.SpinOrbit.Coupling On # On|Off, default=off
scf.ElectronicTemperature 800.0 # default=300 (K)
scf.energycutoff 250.0 # default=150 (Ry)
scf.maxIter 100 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diis # 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 40 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 15
scf.criterion 1.0e-5 # default=1.0e-6 (Hartree)
Why can I get this?Am I set up too many Au atoms in the lead?
And how should I do?
Thanks for your help.
chow
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