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Segmentation fault (signal 11)
Date: 2020/03/29 21:13
Name: VictorS   <victorshevelev@yandex.ru>

Hello everyone. Im new in OpenMX and has a problem with calculation of graphene on Co. Previous calculations of graphene and BN monolayers were good, bulk materials were also calculated. This calculation is stopped after this part,
<UCell_Box> Info. of cutoff energy and num. of grids
lattice vectors (bohr)
A = 4.711040912494, 0.000000000000, 0.000000000000
B = 2.355520456247, 4.079881108494, 0.000000000000
C = 0.000000000000, 0.000000000000, 94.486299428946
reciprocal lattice vectors (bohr^-1)
RA = 1.333714867667, -0.770020637868, 0.000000000000
RB = 0.000000000000, 1.540041275737, 0.000000000000
RC = 0.000000000000, 0.000000000000, 0.066498374316
Required cutoff energy (Ryd) for 3D-grids = 1500.0000
Used cutoff energy (Ryd) for 3D-grids = 1482.3295, 1482.3295, 1528.8916
Num. of grids of a-, b-, and c-axes = 50, 50, 1176

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 5043 RUNNING AT madsuicide-PC
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions






My input file here.





#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name graphene/Co
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
C C6.0-s2p1 C_PBE19
Co Co6.0S-s2p2d2f1 Co_PBE19S
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 17
Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0 0 0 2.0 2.0
2 C 0.333333 0.6666666 0 2.0 2.0
3 Co 0 0 0.04264 9.0 6.0
4 Co 0.333333 0.666666 0.081721 9.0 6.0
5 Co 0.666666 0.333333 0.12297 9.0 6.0
6 Co 0 0 0.16329 9.0 6.0
7 Co 0.333333 0.666666 0.204 9.0 6.0
8 Co 0.666666 0.333333 0.2447 9.0 6.0
9 Co 0 0 0.28543 9.0 6.0
10 Co 0.333333 0.666666 0.32614 9.0 6.0
11 Co 0.666666 0.333333 0.36685 9.0 6.0
12 Co 0 0 0.40717 9.0 6.0
13 Co 0.333333 0.666666 0.44842 9.0 6.0
14 Co 0.666666 0.333333 0.4875 9.0 6.0
15 Co 0 0 0.53014 9.0 6.0
16 C 0 0 0.57 2.0 2.0
17 C 0.6666666 0.33333333 0.57 2.0 2.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
2.49297567 0 0.0000
1.246487835 2.15898026124 0
0.0000 0 50
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization off # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 1500.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 14 14 1 # means n1 x n2 x n3
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 5 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type opt # Nomd|Opt|NVE|NVT_VS|NVT_NH
MD.maxIter 200 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)
<MD.Fixed.XYZ
1 1 1 0
2 1 1 0
3 1 1 0
4 1 1 0
5 1 1 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 1 0
12 1 1 0
13 1 1 0
14 1 1 0
15 1 1 0
16 1 1 0
17 1 1 0
MD.Fixed.XYZ>
#
# Band dispersion
#

Band.dispersion on # on|off, default=off

# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.Nkpath 3
<Band.kpath
1000 0.0 0.0 0.0 0.333232333 -0.333232333 0.0 g K
1000 0.333232333 -0.333232333 0.0 0.5 0 0.0 K M
1000 0.5 0 0.0 0.0 0.0 0.0 M g
Band.kpath>

#
# MO output
#

MO.fileout off # on|off
num.HOMOs 1 # default=2
num.LUMOs 1 # default=2
MO.Nkpoint 2 # default=1
<MO.kpoint
0.0 0.0 0.0
0.0 0.0 0.2
MO.kpoint>

#
# DOS and PDOS
#

Dos.fileout on # on|off, default=off
Dos.Erange -25.0 20.0 # default = -20 20
Dos.Kgrid 12 12 12 # default = Kgrid1 Kgrid2 Kgrid3




If somebody can help me to solve this problem, i will be very glad.
メンテ
Page: [1]

Re: Segmentation fault (signal 11) ( No.1 )
Date: 2020/03/29 22:00
Name: VictorS  <victorshevelev@yandex.ru>

Im sorry, wrong atom coordinates, here is right ones, but i still have the same problem.

#
# File Name
#

System.CurrrentDirectory ./ # default=./
System.Name graphene/Co
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

#
# Definition of Atomic Species
#

Species.Number 2
<Definition.of.Atomic.Species
C C6.0-s2p1 C_CA19
Co Co6.0S-s2p2d2f1 Co_CA19S
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 17
Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0 0 0 2.0 2.0
2 C 0.333333 0.3333333 0 2.0 2.0
3 Co 0.33333 0.3333333 0.04264 9.0 6.0
4 Co 0.666666 0.666666 0.081721 6.0 9.0
5 Co 0.33333 0.3333333 0.12297 6.0 9.0
6 Co 0.666666 0.666666 0.16329 6.0 9.0
7 Co 0.33333 0.3333333 0.204 6.0 9.0
8 Co 0.666666 0.666666 0.2447 6.0 9.0
9 Co 0.33333 0.3333333 0.28543 6.0 9.0
10 Co 0.666666 0.666666 0.32614 6.0 9.0
11 Co 0.33333 0.3333333 0.36685 6.0 9.0
12 Co 0.666666 0.666666 0.40717 6.0 9.0
13 Co 0.33333 0.3333333 0.44842 6.0 9.0
14 Co 0.666666 0.666666 0.4875 6.0 9.0
15 Co 0.33333 0.3333333 0.53014 6.0 9.0
16 C 0.33333 0.3333333 0.57 2.0 2.0
17 C 0 0 0.57 2.0 2.0
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
2.49297567 0 0.0000
1.246487835 2.15898026124 0
0.0000 0 50
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 150.0 # default=150 (Ry)
scf.maxIter 200 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 6 6 1 # means n1 x n2 x n3
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.30 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.400 # default=0.40
scf.Mixing.History 5 # default=5
scf.Mixing.StartPulay 6 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)

#
# MD or Geometry Optimization
#

MD.Type opt # Nomd|Opt|NVE|NVT_VS|NVT_NH
MD.maxIter 200 # default=1
MD.TimeStep 1 # default=0.5 (fs)
MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)
<MD.Fixed.XYZ
1 1 1 0
2 1 1 0
3 1 1 0
4 1 1 0
5 1 1 0
6 1 1 0
7 1 1 0
8 1 1 0
9 1 1 0
10 1 1 0
11 1 1 0
12 1 1 0
13 1 1 0
14 1 1 0
15 1 1 0
16 1 1 0
17 1 1 0
MD.Fixed.XYZ>
#
# Band dispersion
#

Band.dispersion on # on|off, default=off

# if <Band.KPath.UnitCell does not exist,
# the reciprical lattice vector is employed.
Band.Nkpath 3
<Band.kpath
1000 0.0 0.0 0.0 0.333232333 -0.333232333 0.0 g K
1000 0.333232333 -0.333232333 0.0 0.5 0 0.0 K M
1000 0.5 0 0.0 0.0 0.0 0.0 M g
Band.kpath>

#
# MO output
#

MO.fileout off # on|off
num.HOMOs 1 # default=2
num.LUMOs 1 # default=2
MO.Nkpoint 2 # default=1
<MO.kpoint
0.0 0.0 0.0
0.0 0.0 0.2
MO.kpoint>

#
# DOS and PDOS
#

Dos.fileout off # on|off, default=off
Dos.Erange -25.0 20.0 # default = -20 20
Dos.Kgrid 12 12 12 # default = Kgrid1 Kgrid2 Kgrid3
メンテ
Re: Segmentation fault (signal 11) ( No.2 )
Date: 2020/03/30 16:41
Name: Naoya Yamaguchi

Hi,

How about decreasing the memory usage by a lower cutoff energy or a poorer PAO?
And, how much is the RAM on your machine?

Regards,
Naoya Yamaguchi
メンテ
Re: Segmentation fault (signal 11) ( No.3 )
Date: 2020/03/30 18:20
Name: VictorS  <victorshevelev@yandex.ru>

I found, that this error may be related with systemname, i changed Graphene/Co > Graphene_Co and it is worked. But now it cannot calculate density correctly, i will try now to set lower cutoff energy. And im not sure, that basis and potentials are good for such system.
メンテ
Re: Segmentation fault (signal 11) ( No.4 )
Date: 2020/03/30 19:06
Name: Naoya Yamaguchi

>I found, that this error may be related with systemname, i changed Graphene/Co > Graphene_Co and it is worked.

Maybe, opening files was failed. And, if it was the cause, You don't need to reduce the cutoff energy. Although I suggested it, I missed a cutoff energy of 150 Ry in the second case. 150 Ry is sometimes too low.

You may refer to the following for choice of PAOs.
http://www.openmx-square.org/openmx_man3.9/node27.html

Regards,
Naoya Yamaguchi
メンテ
Re: Segmentation fault (signal 11) ( No.5 )
Date: 2020/03/30 20:20
Name: VictorS  <victorshevelev@yandex.ru>

Thank you for comments, i will try to fix it.
メンテ

Page: [1]

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