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Fatal error in NEGF run
Date: 2017/02/21 15:41
Name: Andy   <And.chuck.phy@gmail.com>

Dear Prof. Ozaki and Experts,

I have successfully done the transport calculation in the zigzag graphene nanoribbon without any error. Now, I want to do the transport calculations in the Armchair graphene nanoribbon. I ran both of the leads successfully. When I ran the NEGF file, it gives the fatal error mentioned below:


./negf-7agnr-0.0.tranec0_0_1_3_r.cube ./negf-7agnr-0.0.tranec0_0_1_3_i.cube
./negf-7agnr-0.0.tranec0_0_1_4_r.cube ./negf-7agnr-0.0.tranec0_0_1_4_i.cube
[localhost:11972] *** Process received signal ***
[localhost:11973] *** Process received signal ***
[localhost:11973] Signal: Segmentation fault (11)
[localhost:11973] Signal code: Address not mapped (1)
[localhost:11973] Failing at address: 0x19
[localhost:11972] Signal: Segmentation fault (11)
[localhost:11972] Signal code: Address not mapped (1)
[localhost:11972] Failing at address: 0x19
[localhost:11974] *** Process received signal ***
[localhost:11974] Signal: Segmentation fault (11)
[localhost:11974] Signal code: Address not mapped (1)
[localhost:11974] Failing at address: 0x19
.............................
.............................
.............................
[localhost:11973] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0]
[localhost:11973] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365]
[localhost:11973] [ 2] openmx [0x6ebefd]
[localhost:11973] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511]
[localhost:11973] [ 4] openmx(main+0xddc) [0x430f14]
[localhost:11974] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0]
[localhost:11974] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365]
[localhost:11974] [ 2] openmx [0x6ebefd]
[localhost:11974] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511]
[localhost:11974] [ 4] openmx(main+0xddc) [0x430f14]
[localhost:11974] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb]
[localhost:11974] [ 6] openmx [0x4300aa]
[localhost:11974] *** End of error message ***
[localhost:11973] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb]
[localhost:11973] [ 6] openmx [0x4300aa]
[localhost:11973] *** End of error message ***
[localhost:11972] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0]
[localhost:11972] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365]
[localhost:11972] [ 2] openmx [0x6ebefd]
[localhost:11972] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511]
[localhost:11972] [ 4] openmx(main+0xddc) [0x430f14]
[localhost:11972] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb]
[localhost:11972] [ 6] openmx [0x4300aa]
[localhost:11972] *** End of error message ***
[localhost:11984] *** Process received signal ***
[localhost:11984] Signal: Segmentation fault (11)
[localhost:11984] Signal code: Address not mapped (1)
[localhost:11984] Failing at address: 0x19
[localhost:11984] [ 0] /lib64/tls/libpthread.so.0 [0x31cef0c4f0]
[localhost:11984] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x31cde69365]
[localhost:11984] [ 2] openmx [0x6ebefd]
[localhost:11984] [ 3] openmx(TRAN_Main_Analysis+0xbc9) [0x6e0511]
[localhost:11984] [ 4] openmx(main+0xddc) [0x430f14]
[localhost:11984] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x31cde1c3fb]
[localhost:11984] [ 6] openmx [0x4300aa]
[localhost:11984] *** End of error message ***
[localhost:11965] *** Process received signal ***
[localhost:11965] Signal: Segmentation fault (11)
[localhost:11965] Signal code: Address not mapped (1)
[localhost:11965] Failing at address: 0x19

I am not able to resolve this error. Can you please help me to get rid of this. Your help would be highly appreciated.

best,
Chuck
メンテ
Page: [1]

Re: Fatal error in NEGF run ( No.1 )
Date: 2017/03/02 19:12
Name: T. Ozaki

Hi,

I did calculations with input files:

Lead-L-8ZGNR.dat
Lead-R-8ZGNR.dat
NEGF-8ZGNR-0.3.dat

which are stored in work/negf_example.
I confirmed that all the calculations finished normally.

On the other hand, the error message you had implies that the
error appeared in the part related to the eigenchannel analysis.
Actually, the functionality has been newly added from Ver. 3.8.
So it is likely that there is a program bug in the newly
developed part.

If you do not mind, could you post your input files so that I can
check possible bugs?

Thank you for your cooperation in advance.

Regards,

TO
メンテ
Re: Fatal error in NEGF run ( No.2 )
Date: 2017/03/07 23:52
Name: Fronquer

Dear Prof. Ozaki,

Thank you for your reply. I am pasting here my input files. Three input files are very large so I am pasting SCF electronic system parameters and NEGF file that contains the left and right lead and a central region.


Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>

Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 8.53
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>


#
# SCF or Electronic System
#


scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.001 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)


#
# Band dispersion
#

Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>

Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>


#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3
_______________________________________________________________________________________
___________________________________________________________________
NEGF FIle

System.CurrrentDirectory ./ # default=./
System.Name negf-7agnr-0.0
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)


NEGF.filename.hks.l lead-l-7agnr.hks
NEGF.filename.hks.r lead-r-7agnr.hks

NEGF.SCF.Iter.Band 20
NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1

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

#
# Transmission & Eigen Channel Analysis
#

NEGF.tran.Analysis on # default on
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 1 1 # default= 1 1

NEGF.tran.CurrentDensity on # default on

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 1 # default 1
<NEGF.Channel.energy
0.0
NEGF.Channel.energy>
# default 0.0
NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear)


#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>


#
# Atoms
#

Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU


Atoms.Number 30
<Atoms.SpeciesAndCoordinates
1 H 0.00000000 1.49896799 10.45476799 0.50000000 0.50000000
2 H 0.00000000 1.49896799 12.23323212 0.50000000 0.50000000
3 C 0.00000000 2.45111126 9.89602526 2.10000000 1.90000000
4 C 0.00000000 3.66326134 10.62482532 2.10000000 1.90000000
5 C 0.00000000 2.45111126 12.79197487 2.10000000 1.90000000
6 C 0.00000000 3.66326134 12.06317479 2.10000000 1.90000000
7 C 0.00000000 4.89179041 9.91972866 2.10000000 1.90000000
8 C 0.00000000 6.13044410 10.63467848 2.10000000 1.90000000
9 C 0.00000000 4.89179041 12.76827147 2.10000000 1.90000000
10 C 0.00000000 6.13044409 12.05332163 2.10000000 1.90000000
11 C 0.00000000 7.36138815 9.91884466 2.10000000 1.90000000
12 C 0.00000000 8.59083892 10.63036886 2.10000000 1.90000000
13 C 0.00000000 7.36138815 12.76915547 2.10000000 1.90000000
14 C 0.00000000 8.59083892 12.05763127 2.10000000 1.90000000
15 C 0.00000000 9.82419453 9.91415758 2.10000000 1.90000000
16 C 0.00000000 11.05755015 10.63036886 2.10000000 1.90000000
17 C 0.00000000 9.82419453 12.77384254 2.10000000 1.90000000
18 C 0.00000000 11.05755015 12.05763127 2.10000000 1.90000000
19 C 0.00000000 12.28700091 9.91884465 2.10000000 1.90000000
20 C 0.00000000 13.51794496 10.63467848 2.10000000 1.90000000
21 C 0.00000000 12.28700091 12.76915547 2.10000000 1.90000000
22 C 0.00000000 13.51794497 12.05332163 2.10000000 1.90000000
23 C 0.00000000 14.75659866 9.91972865 2.10000000 1.90000000
24 C 0.00000000 15.98512772 10.62482532 2.10000000 1.90000000
25 C 0.00000000 14.75659865 12.76827147 2.10000000 1.90000000
26 C 0.00000000 15.98512773 12.06317479 2.10000000 1.90000000
27 C 0.00000000 17.19727781 9.89602526 2.10000000 1.90000000
28 C 0.00000000 17.19727781 12.79197487 2.10000000 1.90000000
29 H 0.00000000 18.14942107 10.45476800 0.50000000 0.50000000
30 H 0.00000000 18.14942108 12.23323212 0.50000000 0.50000000
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang # Ang|AU

#<Atoms.UnitVectors
# 0.000 0.000 4.88
# 10.000 0.000 0.000
# 0.000 24.000 0.000
#Atoms.UnitVectors>


#
# Lead-Left
#

LeftLeadAtoms.Number 60
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.00000000 2.37422687 1.36437614 2.50000000 1.50000000
2 C 0.00000000 3.60839082 2.05960208 2.50000000 1.50000000
3 C 0.00000000 2.43376259 4.26115562 2.50000000 1.50000000
4 C 0.00000000 3.63512993 3.52681035 2.50000000 1.50000000
5 C 0.00000000 2.44349640 5.63613271 2.50000000 1.50000000
6 C 0.00000000 3.65991791 6.35381020 2.50000000 1.50000000
7 C 0.00000000 2.45076875 8.52190761 2.50000000 1.50000000
8 C 0.00000000 3.66230931 7.79234988 2.50000000 1.50000000
9 C 0.00000000 4.84318085 1.42797834 2.50000000 1.50000000
10 C 0.00000000 6.10587470 2.04496891 2.50000000 1.50000000
11 C 0.00000000 4.87548695 4.21269140 2.50000000 1.50000000
12 C 0.00000000 6.11332783 3.50164816 2.50000000 1.50000000
13 C 0.00000000 4.88522084 5.64270708 2.50000000 1.50000000
14 C 0.00000000 6.12600371 6.35441190 2.50000000 1.50000000
15 C 0.00000000 4.89180632 8.49445642 2.50000000 1.50000000
16 C 0.00000000 6.12857687 7.77559630 2.50000000 1.50000000
17 C 0.00000000 7.35313902 1.43003935 2.50000000 1.50000000
18 C 0.00000000 8.59714409 2.05896815 2.50000000 1.50000000
19 C 0.00000000 7.35235294 4.20354262 2.50000000 1.50000000
20 C 0.00000000 8.58947845 3.50861616 2.50000000 1.50000000
21 C 0.00000000 7.35570450 5.63863657 2.50000000 1.50000000
22 C 0.00000000 8.58779645 6.34964624 2.50000000 1.50000000
23 C 0.00000000 7.36049316 8.48950565 2.50000000 1.50000000
24 C 0.00000000 8.58955552 7.77723893 2.50000000 1.50000000
25 C 0.00000000 9.82419454 1.35293302 2.50000000 1.50000000
26 C 0.00000000 11.05124499 2.05896815 2.50000000 1.50000000
27 C 0.00000000 9.82419453 4.21523106 2.50000000 1.50000000
28 C 0.00000000 11.05891061 3.50861616 2.50000000 1.50000000
29 C 0.00000000 9.82419453 5.63934129 2.50000000 1.50000000
30 C 0.00000000 11.06059262 6.34964624 2.50000000 1.50000000
31 C 0.00000000 9.82419453 8.49176210 2.50000000 1.50000000
32 C 0.00000000 11.05883355 7.77723893 2.50000000 1.50000000
33 C 0.00000000 12.29525004 1.43003937 2.50000000 1.50000000
34 C 0.00000000 13.54251437 2.04496891 2.50000000 1.50000000
35 C 0.00000000 12.29603613 4.20354261 2.50000000 1.50000000
36 C 0.00000000 13.53506124 3.50164815 2.50000000 1.50000000
37 C 0.00000000 12.29268457 5.63863657 2.50000000 1.50000000
38 C 0.00000000 13.52238535 6.35441190 2.50000000 1.50000000
39 C 0.00000000 12.28789590 8.48950564 2.50000000 1.50000000
40 C 0.00000000 13.51981219 7.77559630 2.50000000 1.50000000
41 C 0.00000000 14.80520821 1.42797831 2.50000000 1.50000000
42 C 0.00000000 16.03999827 2.05960209 2.50000000 1.50000000
43 C 0.00000000 14.77290213 4.21269140 2.50000000 1.50000000
44 C 0.00000000 16.01325914 3.52681034 2.50000000 1.50000000
45 C 0.00000000 14.76316823 5.64270708 2.50000000 1.50000000
46 C 0.00000000 15.98847116 6.35381019 2.50000000 1.50000000
47 C 0.00000000 14.75658274 8.49445642 2.50000000 1.50000000
48 C 0.00000000 15.98607975 7.79234988 2.50000000 1.50000000
49 C 0.00000000 17.27416221 1.36437613 2.50000000 1.50000000
50 C 0.00000000 17.21462647 4.26115561 2.50000000 1.50000000
51 C 0.00000000 17.20489266 5.63613270 2.50000000 1.50000000
52 C 0.00000000 17.19762032 8.52190761 2.50000000 1.50000000
53 H 0.00000000 1.58490677 2.17980351 0.50000000 0.50000000
54 H 0.00000000 1.48154811 3.69397693 0.50000000 0.50000000
55 H 0.00000000 1.49586602 6.20324257 0.50000000 0.50000000
56 H 0.00000000 1.49842826 7.96335252 0.50000000 0.50000000
57 H 0.00000000 18.06348229 2.17980351 0.50000000 0.50000000
58 H 0.00000000 18.16684095 3.69397694 0.50000000 0.50000000
59 H 0.00000000 18.15252305 6.20324258 0.50000000 0.50000000
60 H 0.00000000 18.14996080 7.96335253 0.50000000 0.50000000
LeftLeadAtoms.SpeciesAndCoordinates>


#
# Lead-Right
#


RightLeadAtoms.Number 60
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 H 0.00000000 1.49842826 14.72464760 0.50000000 0.50000000
2 H 0.00000000 1.49586602 16.48475754 0.50000000 0.50000000
3 H 0.00000000 1.48154811 18.99402317 0.50000000 0.50000000
4 H 0.00000000 1.58490676 20.50819659 0.50000000 0.50000000
5 C 0.00000000 2.45076875 14.16609249 1.50000000 2.50000000
6 C 0.00000000 3.66230931 14.89565025 1.50000000 2.50000000
7 C 0.00000000 2.44349640 17.05186740 1.50000000 2.50000000
8 C 0.00000000 3.65991791 16.33418993 1.50000000 2.50000000
9 C 0.00000000 2.43376259 18.42684451 1.50000000 2.50000000
10 C 0.00000000 3.63512993 19.16118977 1.50000000 2.50000000
11 C 0.00000000 2.37422685 21.32362399 1.50000000 2.50000000
12 C 0.00000000 3.60839080 20.62839803 1.50000000 2.50000000
13 C 0.00000000 4.89180632 14.19354369 1.50000000 2.50000000
14 C 0.00000000 6.12857687 14.91240382 1.50000000 2.50000000
15 C 0.00000000 4.88522084 17.04529304 1.50000000 2.50000000
16 C 0.00000000 6.12600371 16.33358822 1.50000000 2.50000000
17 C 0.00000000 4.87548694 18.47530872 1.50000000 2.50000000
18 C 0.00000000 6.11332783 19.18635197 1.50000000 2.50000000
19 C 0.00000000 4.84318085 21.26002178 1.50000000 2.50000000
20 C 0.00000000 6.10587470 20.64303121 1.50000000 2.50000000
21 C 0.00000000 7.36049316 14.19849447 1.50000000 2.50000000
22 C 0.00000000 8.58955552 14.91076119 1.50000000 2.50000000
23 C 0.00000000 7.35570450 17.04936355 1.50000000 2.50000000
24 C 0.00000000 8.58779645 16.33835388 1.50000000 2.50000000
25 C 0.00000000 7.35235294 18.48445751 1.50000000 2.50000000
26 C 0.00000000 8.58947845 19.17938397 1.50000000 2.50000000
27 C 0.00000000 7.35313902 21.25796078 1.50000000 2.50000000
28 C 0.00000000 8.59714408 20.62903197 1.50000000 2.50000000
29 C 0.00000000 9.82419453 14.19623802 1.50000000 2.50000000
30 C 0.00000000 11.05883355 14.91076119 1.50000000 2.50000000
31 C 0.00000000 9.82419453 17.04865884 1.50000000 2.50000000
32 C 0.00000000 11.06059262 16.33835388 1.50000000 2.50000000
33 C 0.00000000 9.82419453 18.47276907 1.50000000 2.50000000
34 C 0.00000000 11.05891061 19.17938397 1.50000000 2.50000000
35 C 0.00000000 9.82419453 21.33506711 1.50000000 2.50000000
36 C 0.00000000 11.05124498 20.62903197 1.50000000 2.50000000
37 C 0.00000000 12.28789590 14.19849448 1.50000000 2.50000000
38 C 0.00000000 13.51981220 14.91240382 1.50000000 2.50000000
39 C 0.00000000 12.29268456 17.04936355 1.50000000 2.50000000
40 C 0.00000000 13.52238536 16.33358822 1.50000000 2.50000000
41 C 0.00000000 12.29603613 18.48445751 1.50000000 2.50000000
42 C 0.00000000 13.53506124 19.18635197 1.50000000 2.50000000
43 C 0.00000000 12.29525005 21.25796078 1.50000000 2.50000000
44 C 0.00000000 13.54251437 20.64303122 1.50000000 2.50000000
45 C 0.00000000 14.75658274 14.19354369 1.50000000 2.50000000
46 C 0.00000000 15.98607976 14.89565025 1.50000000 2.50000000
47 C 0.00000000 14.76316823 17.04529304 1.50000000 2.50000000
48 C 0.00000000 15.98847116 16.33418992 1.50000000 2.50000000
49 C 0.00000000 14.77290212 18.47530872 1.50000000 2.50000000
50 C 0.00000000 16.01325915 19.16118977 1.50000000 2.50000000
51 C 0.00000000 14.80520823 21.26002178 1.50000000 2.50000000
52 C 0.00000000 16.03999826 20.62839804 1.50000000 2.50000000
53 C 0.00000000 17.19762032 14.16609249 1.50000000 2.50000000
54 C 0.00000000 17.20489267 17.05186740 1.50000000 2.50000000
55 C 0.00000000 17.21462648 18.42684451 1.50000000 2.50000000
56 C 0.00000000 17.27416222 21.32362398 1.50000000 2.50000000
57 H 0.00000000 18.14996080 14.72464760 0.50000000 0.50000000
58 H 0.00000000 18.15252305 16.48475753 0.50000000 0.50000000
59 H 0.00000000 18.16684096 18.99402318 0.50000000 0.50000000
60 H 0.00000000 18.06348230 20.50819661 0.50000000 0.50000000
RightLeadAtoms.SpeciesAndCoordinates>

#
# SCF or Electronic System
#


scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 2000 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 20.0 # default=1
scf.Init.Mixing.Weight 0.1 # default=0.30
scf.Min.Mixing.Weight 0.04 # default=0.001
scf.Max.Mixing.Weight 0.4 # default=0.40
scf.Mixing.History 60 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)


#
# MD or Geometry Optimization
#

MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 10 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 200 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)

Please have a look and help me in overcoming to this problem.
Thanking you.



メンテ
Re: Fatal error in NEGF run ( No.3 )
Date: 2017/03/08 14:59
Name: T. Ozaki

Hi,

It turned out that this is actually caused by a bug that memory deallocation
is improperly performed in TRAN_Main_Analysis.c.

The bug has been fixed and the patch is available as patch3.8.3.tar.gz at
http://www.openmx-square.org/download.html

Thank you for your feedback and cooperation.

Regards,

TO
メンテ
Re: Fatal error in NEGF run ( No.4 )
Date: 2017/03/14 07:01
Name: ali

i have the same problem and i use the new patch but the problem exist.
メンテ
Re: Fatal error in NEGF run ( No.5 )
Date: 2017/03/14 15:36
Name: ali

Dear developers
i applied new patch but the bug did not fixed?
what should i do?
thanks
メンテ
Re: Fatal error in NEGF run ( No.6 )
Date: 2017/03/14 15:54
Name: T. Ozaki

Hi,

If you do not mind, cloud you share your input files which caused the problem?

Regards,

TO

P.S.
The problem does not cause serious trouble for your final results,
since this happens at the end of the code where memory deallocations
are performed.
メンテ
Re: Fatal error in NEGF run ( No.7 )
Date: 2017/03/14 16:47
Name: ali

hi

System.CurrrentDirectory ./ # default=./

System.Name ngf-0.0
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p2d1 C_CA13
N N5.0-s2p2d1 N_CA13
Definition.of.Atomic.Species>

NEGF.filename.hks.l lead.hks
NEGF.filename.hks.r lead.hks

NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1

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)
NEGF.scf.Iter.Band 20




NEGF.tran.energydiv 200 # default=200
NEGF.tran.energyrange -10.0 10.0 5.0e-3 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1

Atoms.Number 29
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU

<Atoms.SpeciesAndCoordinates
1 C 9.2009321 3.0665410 7.6944084 2.00000 2.00000
2 C 9.2180813 0.6127711 7.6910203 2.00000 2.00000
3 C 9.9230181 1.8475303 7.6879522 2.00000 2.00000
4 C 9.9222386 4.2852240 7.6842867 2.00000 2.00000
5 C 11.3356511 1.7893617 7.6782112 2.00000 2.00000
6 C 11.3348041 4.3424755 7.6707664 2.00000 2.00000
7 N 11.9517960 0.6112769 7.6639009 2.50000 2.50000
8 N 12.0784601 3.0675667 7.6825771 2.50000 2.50000
9 C 13.4989073 3.0651358 7.7596100 2.00000 2.00000
10 N 14.1548404 4.2277609 7.6536692 2.50000 2.50000
11 N 14.1140825 1.8949232 7.9088371 2.50000 2.50000
12 C 15.4019534 4.2073312 8.0919982 2.00000 2.00000
13 C 15.4019771 1.9312983 8.1752629 2.00000 2.00000
14 N 16.0456234 3.0821314 8.4735999 2.50000 2.50000
15 N 16.1088921 0.6147233 8.1460947 2.50000 2.50000
16 C 17.5282627 0.6148996 8.0504150 2.00000 2.00000
17 N 18.1540095 1.7842448 8.0857851 2.50000 2.50000
18 N 18.1650615 4.3606991 7.8678134 2.50000 2.50000
19 C 19.4633695 1.7518032 8.2416761 2.00000 2.00000
20 C 19.4549595 4.3821546 8.1696274 2.00000 2.00000
21 N 20.1267445 0.6017957 8.4869103 2.50000 2.50000
22 N 20.1664314 3.0667473 8.1521931 2.50000 2.50000
23 C 21.5731076 3.0686110 7.9471351 2.00000 2.00000
24 N 22.1939245 4.2309451 7.7344599 2.50000 2.50000
25 N 22.2143785 1.9029856 7.9558298 2.50000 2.50000
26 C 23.4932174 4.2748061 7.7166978 2.00000 2.00000
27 C 23.5018150 1.8598120 7.8001596 2.00000 2.00000
28 N 24.2570850 3.0673182 7.7406987 2.50000 2.50000
29 N 24.1886586 0.6123005 7.7060660 2.50000 2.50000
Atoms.SpeciesAndCoordinates>

LeftLeadAtoms.Number 16
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.7083626 3.0673063 7.7029471 2.00000 2.00000
2 C 0.7083626 0.6134413 7.7029454 2.00000 2.00000
3 C 1.4166265 1.8404224 7.7029714 2.00000 2.00000
4 C 1.4166265 4.2942874 7.7029712 2.00000 2.00000
5 C 2.8334116 1.8404223 7.7029785 2.00000 2.00000
6 C 2.8334116 4.2942873 7.7029795 2.00000 2.00000
7 C 3.5416756 0.6134413 7.7029482 2.00000 2.00000
8 C 3.5416756 3.0673062 7.7029482 2.00000 2.00000
9 C 4.9584126 3.0673063 7.7029371 2.00000 2.00000
10 C 4.9584126 0.6134413 7.7029354 2.00000 2.00000
11 C 5.6666765 1.8404224 7.7029614 2.00000 2.00000
12 C 5.6666765 4.2942874 7.7029612 2.00000 2.00000
13 C 7.0834616 1.8404223 7.7029685 2.00000 2.00000
14 C 7.0834616 4.2942873 7.7029695 2.00000 2.00000
15 C 7.7917256 0.6134413 7.7029382 2.00000 2.00000
16 C 7.7917256 3.0673062 7.7029382 2.00000 2.00000
LeftLeadAtoms.SpeciesAndCoordinates>


#
# Lead-Right
#
RightLeadAtoms.Number 16
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 25.6357771 3.0673063 7.7029171 2.00000 2.00000
2 C 25.6357771 0.6134413 7.7029154 2.00000 2.00000
3 C 26.3440410 1.8404224 7.7029414 2.00000 2.00000
4 C 26.3440410 4.2942874 7.7029412 2.00000 2.00000
5 C 27.7608261 1.8404223 7.7029485 2.00000 2.00000
6 C 27.7608261 4.2942873 7.7029495 2.00000 2.00000
7 C 28.4690901 0.6134413 7.7029182 2.00000 2.00000
8 C 28.4690901 3.0673062 7.7029182 2.00000 2.00000
9 C 29.8858271 3.0673063 7.7029071 2.00000 2.00000
10 C 29.8858271 0.6134413 7.7029054 2.00000 2.00000
11 C 30.5940910 1.8404224 7.7029314 2.00000 2.00000
12 C 30.5940910 4.2942874 7.7029312 2.00000 2.00000
13 C 32.0108761 1.8404223 7.7029385 2.00000 2.00000
14 C 32.0108761 4.2942873 7.7029395 2.00000 2.00000
15 C 32.7191401 0.6134413 7.7029082 2.00000 2.00000
16 C 32.7191401 3.0673062 7.7029082 2.00000 2.00000
RightLeadAtoms.SpeciesAndCoordinates>

#
# SCF or Electronic System
#

scf.XcType LDA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 150.0 # default=150 (Ry)

scf.maxIter 1000 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.ProExpn.VNA on # default=on
scf.lapack.dste dstevx # dstegr|dstedc|dstevx,
scf.Mixing.Type Rmm-Diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.1 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
#scf.Kerker.factor 1.0 # default=1.0
scf.Mixing.History 5 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.Mixing.EveryPulay 5 # default=5
scf.criterion 1.0e-6 # default=1.0e-6 (Hartree)




and the error


Parameters for the integration of the non-equilibrium part
lower bound: -3.607282740421 (eV)
upper bound: -3.607282740421 (eV)
energy step: 0.020000000000 (eV)
number of steps: 0
Warning: the energy step you specified is larger than the integration range.
[mmhs:02848] *** Process received signal ***
[mmhs:02848] Signal: Segmentation fault (11)
[mmhs:02848] Signal code: Address not mapped (1)
[mmhs:02848] Failing at address: 0x29
[mmhs:02848] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10330) [0x7fa870106330]
[mmhs:02848] [ 1] openmx() [0x6875ba]
[mmhs:02848] [ 2] openmx() [0x4177e1]
[mmhs:02848] [ 3] openmx() [0x43b188]
[mmhs:02848] [ 4] openmx() [0x408783]
[mmhs:02848] [ 5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fa86fd52f45]
[mmhs:02848] [ 6] openmx() [0x4096f5]
[mmhs:02848] *** End of error message ***
Segmentation fault


メンテ
Re: Fatal error in NEGF run ( No.8 )
Date: 2017/03/14 17:56
Name: T. Ozaki

Hi,

Please share all the input files for left and right reads and NEGF calculations.
Otherwise, it is difficult to reproduce your problem.

Regards,

TO
メンテ
Re: Fatal error in NEGF run ( No.9 )
Date: 2017/03/15 02:47
Name: ali

Dear Prof. Ozaki

The bug fixed. I had a mistake in lead file.
thank you for your support and guidance.

メンテ
Re: Fatal error in NEGF run ( No.10 )
Date: 2017/03/14 18:55
Name: Fronquer

Dear Prof. Ozaki,

I have successfully installed the patch and the problem is fixed.

Thanks a lot.

Regards,

Fronquer
メンテ

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