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Error code in running GGA-PBE+U
Date: 2022/02/28 10:41
Name: Vipin Kumar

Dear All,

I am getting following error code while running GGA-PBE+U

*********************************************
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 *******************
<Band> Solving the eigenvalue problem...
KGrids1: -0.41667 -0.25000 -0.08333 0.08333 0.25000 0.41667
KGrids2: -0.41667 -0.25000 -0.08333 0.08333 0.25000 0.41667
KGrids3: -0.37500 -0.12500 0.12500 0.37500
<Band_DFT> Eigen, time=0.591670
<Band_DFT> DM, time=0.974561
1 Ni MulP 8.5219 8.5219 sum 17.0438
2 H MulP 0.2365 0.2365 sum 0.4730
3 H MulP 0.2365 0.2365 sum 0.4730
4 O MulP 3.5025 3.5025 sum 7.0051
5 O MulP 3.5025 3.5025 sum 7.0051
Sum of MulP: up = 16.00000 down = 16.00000
total= 32.00000 ideal(neutral)= 32.00000
[msrc:27342] *** Process received signal ***
[msrc:27351] *** Process received signal ***
[msrc:27351] Signal: Segmentation fault (11)
[msrc:27351] Signal code: Address not mapped (1)
[msrc:27351] Failing at address: 0x8
[msrc:27342] Signal: Segmentation fault (11)
[msrc:27342] Signal code: Address not mapped (1)
[msrc:27342] Failing at address: 0x8
[msrc:27351] [msrc:27342] [ 0] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f52c809c8a0]
[msrc:27342] [ 1] /lib/x86_64-linux-gnu/libpthread.so.0openmx(+0x1b34c3)[0x559f4e1cb4c3]
[msrc:27342] [ 2] openmx(+0x7287c)[0x559f4e08a87c]
[msrc:27342] [ 3] [msrc:27368] *** Process received signal ***
openmx(+0x1240f)[0x559f4e02a40f]
[msrc:27342] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f52c7cbab97]
[msrc:27342] [ 5] openmx(+0x12d8a)[0x559f4e02ad8a]
[msrc:27341] *** Process received signal ***
[msrc:27341] Signal: Segmentation fault (11)
[msrc:27341] Signal code: Address not mapped (1)
[msrc:27341] Failing at address: 0x8
(+0x128a0)[0x7fb79295d8a0]
[msrc:27351] [ 1] openmx(+0x1b34c3)[0x55ea636d84c3]
[msrc:27351] [ 2] openmx(+0x7287c[msrc:27342] *** End of error message ***
)[0x55ea6359787c]
[msrc:27351] [ 3] [msrc:27343] *** Process received signal ***
[msrc:27343] Signal: Segmentation fault (11)
[msrc:27343] Signal code: Address not mapped (1)
[msrc:27343] Failing at address: 0x8
[msrc:27368] Signal: Segmentation fault (11)
[msrc:27368] Signal code: Address not mapped (1)
[msrc:27368] Failing at address: 0x8
openmx(+0x1240f)[0x55ea6353740f]
[msrc:27351] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fb79257bb97]
[msrc:27351] [ 5] openmx(+0x12d8a)[0x55ea63537d8a]
[msrc:27351] *** End of error message ***
[msrc:27343] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f893e5d58a0]
[msrc:27343] [ 1] openmx(+0x1b34c3)[0x563dc1e304c3]
[msrc:27343] [msrc:27368] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f500742f8a0]
[msrc:27368] [ 1] openmx(+0x1b34c3[ 2] openmx(+0x7287c)[0x563dc1cef87c]
[msrc:27343] [ 3] openmx(+0x1240f)[0x)[0x5580e793c4c3]
[msrc:27368] [ 2] openmx(563dc1c8f40f]
[msrc:27343] +0x7287c)[0x5580e77fb87c]
[msrc:27368] [ 3] openmx(+0x1240f)[0x5580e779b40f]
[msrc:27368] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f893e1f3b97]
[msrc:27343] [ 5] openmx(+0x12d8a)[0x563dc1c8fd8a]
[msrc:27343] *** End of error message ***
[ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f500704db97]
[msrc:27368] [ 5] openmx(+0x12d8a)[0x5580e779bd8a]
[msrc:27368] *** End of error message ***
[msrc:27341] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7f6ec8e798a0]
[msrc:27341] [ 1] openmx(+0x1b34c3)[0x5614d11bb4c3]
[msrc:27341] [ 2] openmx(+0x7287c)[0x5614d107a87c]
[msrc:27341] [ 3] openmx(+0x1240f)[0x5614d101a40f]
[msrc:27341] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f6ec8a97b97]
[msrc:27341] [ 5] openmx(+0x12d8a)[0x5614d101ad8a]
[msrc:27341] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node msrc exited on signal 11 (Segmentation fault).


Below is the input file:

#
# This was generated by OpenMX Viewer
DATA.PATH /home/msrc/OPEN/openmx3.9/DFT_DATA19
System.CurrrentDirectory ./
System.Name NioH2
level.of.stdout 1
level.of.fileout 1

Species.Number 3
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE19
O O6.0-s2p2d1 O_PBE19
Ni Ni6.0H-s3p2d1 Ni_PBE19H
Definition.of.Atomic.Species>


<Hubbard.U.values # eV
H 1s 0.0 2s 0.0 1p 0.0
O 1s 0.0 2s 0.0 1p 0.0 2p 0.0 1d 0.0
Ni 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 5.0
Hubbard.U.values>

<Hund.J.values # eV
H 1s 0.0 2s 0.0 1p 0.0
O 1s 0.0 2s 0.0 1p 0.0 2p 0.0 1d 0.0
Ni 1s 0.0 2s 0.0 3s 0.0 1p 0.0 2p 0.0 1d 0.5
Hund.J.values>


Atoms.Number 5
Atoms.SpeciesAndCoordinates.Unit FRAC
<Atoms.SpeciesAndCoordinates
1 Ni 0.0000000 0.0000000 0.0000000 9.0 9.0 off
2 H 0.6666667 0.3333333 0.5733480 0.5 0.5 off
3 H 0.3333333 0.6666667 0.4266520 0.5 0.5 off
4 O 0.6666667 0.3333333 0.7813790 3.0 3.0 off
5 O 0.3333333 0.6666667 0.2186210 3.0 3.0 off
Atoms.SpeciesAndCoordinates>

Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
3.1654862 0.0000000 0.0000000
-1.5827431 2.7413915 0.0000000
0.0000000 0.0000000 4.6768641
Atoms.UnitVectors>

scf.XcType GGA-PBE
scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 220.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 6 6 4
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7

MD.Type nomd
MD.maxIter 1
MD.TimeStep 1.0
MD.Opt.criterion 0.0003


Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
9.7179656 0.0000000 0.0000000
-4.8589828 8.4160051 0.0000000
0.0000000 0.0000000 4.5159990
Atoms.UnitVectors>

scf.XcType GGA-PBE

scf.Hubbard.U On # On|Off, default=off
scf.Hubbard.Occupation dual # onsite|full|dual, default=dual
scf.DFTU.Type 2 # 1:Simplified(Dudarev)|2:General, default=1
scf.dc.Type cFLL # sFLL|sAMF|cFLL|cAMF, default=sFLL
scf.Slater.Ratio 0.625 # default=0.625
scf.Yukawa off # default=off

scf.SpinPolarization off
scf.ElectronicTemperature 300.0
scf.energycutoff 220.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 2 2 4
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15
scf.criterion 1.0e-7

MD.Type nomd
MD.maxIter 1
MD.TimeStep 1.0
MD.Opt.criterion 0.0003



Band.dispersion on
Band.Nkpath 3
<Band.kpath
30 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 G M
17 0.500000 0.000000 0.000000 0.333333 0.333333 0.000000 M K
34 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 K G
Band.kpath>

Dos.fileout on
Dos.Erange -6.0 6.0
Dos.Kgrid 45 45 1

Could you please help me in some way?

Regards,
Vipin
メンテ
Page: [1]

Re: Error code in running GGA-PBE+U ( No.1 )
Date: 2022/03/01 12:48
Name: Naoya Yamaguchi

Hi,

It seems that `scf.DFTU.Type 2` is not compatible with `scf.SpinPolarization off`. Please use `scf.DFTU.Type 1` or `scf.SpinPolarization on`.

Regards,
Naoya Yamaguchi
メンテ

Page: [1]

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