Error in BSE calculation

Deals with issues related to computation of optical spectra in reciprocal space: RPA, TDDFT, local field effects.

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Jagjit Kaur
Posts: 20
Joined: Fri Apr 16, 2021 12:51 pm

Error in BSE calculation

Post by Jagjit Kaur » Sun Apr 18, 2021 6:15 pm

I am getting an error when I am running the second step of BSE i.e. BS Kernel

The error is given by:

-> [05.02] Independent Particles properties @q1
<---> [DIP] Checking dipoles header
<---> [05.03] BSE Kernel @q1 (Resonant CORRRELATION EXCHANGE)
<---> [05.03.01] Screened interaction header I/O[qmobile:04495] *** Process received signal ***
[qmobile:04495] Signal: Segmentation fault (11)
[qmobile:04495] Signal code: Address not mapped (1)
[qmobile:04495] Failing at address: 0x4
[qmobile:04495] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12890)[0x7fa8d88bc890]
[qmobile:04495] [ 1] yambo(+0x64720)[0x563742c79720]
[qmobile:04495] [ 2] yambo(+0x4ce23)[0x563742c61e23]
[qmobile:04495] [ 3] yambo(+0x3b870)[0x563742c50870]
[qmobile:04495] [ 4] yambo(+0x3960c)[0x563742c4e60c]
[qmobile:04495] [ 5] yambo(+0x2ecfd8)[0x563742f01fd8]
[qmobile:04495] [ 6] yambo(+0x37909)[0x563742c4c909]
[qmobile:04495] [ 7] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fa8d84dab97]
[qmobile:04495] [ 8] yambo(+0x379ba)[0x563742c4c9ba]
[qmobile:04495] *** End of error message ***
Segmentation fault (core dumped)

The input file is:
__ __ ______ __ __ _______ ______
# | \ / \ / \ | \ / \| \ / \
# \$$\ / $$| $$$$$$\| $$\ / $$| $$$$$$$\| $$$$$$\
# \$$\/ $$ | $$__| $$| $$$\ / $$$| $$__/ $$| $$ | $$
# \$$ $$ | $$ $$| $$$$\ $$$$| $$ $$| $$ | $$
# \$$$$ | $$$$$$$$| $$\$$ $$ $$| $$$$$$$\| $$ | $$
# | $$ | $$ | $$| $$ \$$$| $$| $$__/ $$| $$__/ $$
# | $$ | $$ | $$| $$ \$ | $$| $$ $$ \$$ $$
# \$$ \$$ \$$ \$$ \$$ \$$$$$$$ \$$$$$$
#
# Version 5.0.1 Revision 19550 Hash 8959025f8
# Branch is master
# MPI+SLK+SLEPC+HDF5_IO Build
# http://www.yambo-code.org
#
optics # [R] Linear Response optical properties
bse # [R][BSE] Bethe Salpeter Equation.
dipoles # [R] Oscillator strenghts (or dipoles)
BSEmod= "resonant" # [BSE] resonant/retarded/coupling
BSKmod= "SEX" # [BSE] IP/Hartree/HF/ALDA/SEX/BSfxc
BSENGexx= 30 Ry # [BSK] Exchange components
BSENGBlk= 4 Ry # [BSK] Screened interaction block size [if -1 uses all the G-vectors of W(q,G,Gp)]
#WehCpl # [BSK] eh interaction included also in coupling
BSEprop= "abs" # [BSS] abs/kerr/magn/dichr trace
% BSEQptR
1 | 1 | # [BSK] Transferred momenta range
%
% BSEBands
6 | 10 | # [BSK] Bands range
%

The report file is given by:



** ** ** **** **** ****** *******
//** ** **** /**/** **/** /*////** **/////**
//**** **//** /**//** ** /** /* /** ** //**
//** ** //** /** //*** /** /****** /** /**
/** **********/** //* /** /*//// **/** /**
/** /**//////**/** / /** /* /**//** **
/** /** /**/** /** /******* //*******
// // // // // /////// ///////

Version 5.0.1 Revision 19550 Hash 8959025f8
Branch is master
MPI+SLK+SLEPC+HDF5_IO Build
http://www.yambo-code.org

04/15/2021 at 17:00 yambo @ qmobile
==================================================

Cores : 1
Threads per core : 1
Threads total : 1
Nodes Computing : 1
Nodes IO : 1

Fragmented WFs : yes
CORE databases : .
Additional I/O : .
Communications : .
Input file : 02_3D_BSE_kernel.in
Report file : ./r-3D_BSE_optics_dipoles_bse
Verbose log/report : no

Job string : 3D_BSE

Precision : SINGLE

[RD./SAVE//ns.db1]--------------------------------------------------------------
Bands : 100
K-points : 14
G-vectors : 8029 [RL space]
Components : 1016 [wavefunctions]
Symmetries : 24 [spatial+T-reV]
Spinor components : 1
Spin polarizations : 1
Temperature : 0.000000 [eV]
Electrons : 16.00000
WF G-vectors : 1477
Max atoms/species : 2
No. of atom species : 2
Magnetic symmetries : no
- S/N 003471 ---------------------------------------------- v.04.01.02 r.14024 -

[02] CORE Variables Setup
=========================


[02.01] Unit cells
==================

Cell kind : HCP
Atoms in the cell : B N
number of B atoms : 2
number of N atoms : 2
Alat factors : 4.71600 4.08418 12.17671 [a.u.]

Direct lattice volume : 234.5353 [a.u.]
Direct lattice vectors: A[ 1 ] A[ 2 ] A[ 3 ]
A[ 1 ]: 1.000000 0.000000 0.000000 [iru]
A[ 2 ]: -0.500000 1.000000 0.000000 [iru]
A[ 3 ]: 0.000000 0.000000 1.000000 [iru]

Recip. lattice volume : 1.057624 [a.u.]
Recip. lattice vectors: B[ 1 ] B[ 2 ] B[ 3 ]
B[ 1 ]: 1.000000 0.500000 0.000000 [iku]
B[ 2 ]: 0.000000 1.000000 0.000000 [iku]
B[ 3 ]: 0.000000 0.000000 1.000000 [iku]

[02.02] Symmetries
==================

Inversion symmetry : yes
Spatial inversion : no
Inversion index : 13
K-space Time-reversal : yes
Magnetic symmetries : no
Time-reversal derived K-space symmetries: 13 24
Group table correct : yes
Symmetries units : [cc]
: 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000
: -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000
: -0.500000 0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 1.000000
: -0.500000 -0.866025 0.000000 0.866025 -0.500000 0.000000 0.000000 0.000000 1.000000
: 0.500000 -0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 -1.000000
: 0.500000 0.866025 0.000000 0.866025 -0.500000 0.000000 0.000000 0.000000 -1.000000
: 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -1.000000
: -1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000
: -0.500000 -0.866025 0.000000 0.866025 -0.500000 0.000000 0.000000 0.000000 -1.000000
: -0.500000 0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 -1.000000
[S 11]: 0.500000 0.866025 0.000000 0.866025 -0.500000 0.000000 0.000000 0.000000 1.000000
[S 12]: 0.500000 -0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 1.000000
[S*13]: -1.000000 -0.000000 -0.000000 -0.000000 -1.000000 -0.000000 -0.000000 -0.000000 -1.000000
[S*14]: 1.000000 -0.000000 -0.000000 -0.000000 -1.000000 -0.000000 -0.000000 -0.000000 1.000000
[S*15]: 0.500000 -0.866025 -0.000000 0.866025 0.500000 -0.000000 -0.000000 -0.000000 -1.000000
[S*16]: 0.500000 0.866025 -0.000000 -0.866025 0.500000 -0.000000 -0.000000 -0.000000 -1.000000
[S*17]: -0.500000 0.866025 -0.000000 0.866025 0.500000 -0.000000 -0.000000 -0.000000 1.000000
[S*18]: -0.500000 -0.866025 -0.000000 -0.866025 0.500000 -0.000000 -0.000000 -0.000000 1.000000
[S*19]: -1.000000 -0.000000 -0.000000 -0.000000 -1.000000 -0.000000 -0.000000 -0.000000 1.000000
[S*20]: 1.000000 -0.000000 -0.000000 -0.000000 -1.000000 -0.000000 -0.000000 -0.000000 -1.000000
[S*21]: 0.500000 0.866025 -0.000000 -0.866025 0.500000 -0.000000 -0.000000 -0.000000 1.000000
[S*22]: 0.500000 -0.866025 -0.000000 0.866025 0.500000 -0.000000 -0.000000 -0.000000 1.000000
[S*23]: -0.500000 -0.866025 -0.000000 -0.866025 0.500000 -0.000000 -0.000000 -0.000000 -1.000000
[S*24]: -0.500000 0.866025 -0.000000 0.866025 0.500000 -0.000000 -0.000000 -0.000000 -1.000000

[02.03] Reciprocal space
========================

nG shells : 217
nG charge : 3187
nG WFs : 1477
nC WFs : 1016
G-vecs. in first 21 shells: [ Number ]
1 3 5 11 13 25 37 39 51
63 65 71 83 95 107 113 125 127
139 151 163
...
Shell energy in first 21 shells: [ mHa ]
0.00000 133.128 532.512 1183.37 1198.15 1316.50 1715.88 2130.05 2381.52
3313.42 3328.20 3550.11 3683.24 4082.62 4511.57 4733.48 4748.27 4792.61
4866.61 5266.00 5680.16
...

[02.04] K-grid lattice
======================

Compatible Grid is : 3D
Base K vectors : K_min[ 1 ] K_min[ 2 ] K_min[ 3 ]
K_min[ 1 ] : 0.000000 -0.166667 0.000000 [rlu]
K_min[ 2 ] : 0.166667 -0.149012E-7 0.00000 [rlu]
K_min[ 3 ] : 0.000000 0.000000 -0.500000 [rlu]
Grid dimensions : 6 6 2
K lattice UC volume : 0.014689 [a.u.]

[02.05] Energies & Occupations
==============================

[X] === General ===
[X] Electronic Temperature : 0.000000 0.000000 [eV K]
[X] Bosonic Temperature : 0.000000 0.000000 [eV K]
[X] Finite Temperature mode : no
[X] El. density : 0.46037E+24 [cm-3]
[X] Fermi Level : 5.110835 [eV]

[X] === Gaps and Widths ===
[X] Conduction Band Min : 3.877976 [eV]
[X] Valence Band Max : 0.000000 [eV]
[X] Filled Bands : 8
[X] Empty Bands : 9 100
[X] Direct Gap : 4.289853 [eV]
[X] Direct Gap localized at k-point : 7
[X] Indirect Gap : 3.877976 [eV]
[X] Indirect Gap between k-points : 14 7
[X] Last valence band width : 3.401086 [eV]
[X] 1st conduction band width : 4.266292 [eV]



[03] Transferred momenta grid and indexing
==========================================

[RD./SAVE//ndb.kindx]-----------------------------------------------------------
Fragmentation : no
Polarization last K : 14
QP states : 1 14
X grid is uniform : yes
Grids : X S
*ERR*BS scattering : no
COLL scattering : no
Sigma scattering : yes
X scattering : yes
- S/N 003471 ---------------------------------------------- v.05.00.01 r.19550 -
[BZ sampling] Q-grid is User defined and/or read from the database

IBZ Q-points : 14
BZ Q-points : 72

K/Q-points units:
rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units

Q [ 1]: 0.000000 0.000000 0.000000 [rlu]
Q [ 2]: 0.000000 0.000000 -0.500000 [rlu]
Q [ 3]: 0.000000 0.166667 0.000000 [rlu]
Q [ 4]: 0.000000 0.166667 -0.500000 [rlu]
Q [ 5]: 0.000000 0.333333 0.000000 [rlu]
Q [ 6]: 0.000000 0.333333 -0.500000 [rlu]
Q [ 7]: 0.000000 -0.500000 0.000000 [rlu]
Q [ 8]: 0.000000 -0.500000 -0.500000 [rlu]
Q [ 9]: 0.166667 0.166667 0.000000 [rlu]
Q [10]: 0.166667 0.166667 -0.500000 [rlu]
Q [11]: 0.166667 0.333333 0.000000 [rlu]
Q [12]: 0.166667 0.333333 -0.500000 [rlu]
Q [13]: 0.333333 0.333333 0.000000 [rlu]
Q [14]: 0.333333 0.333333 -0.500000 [rlu]

[03.01] X + BSE indexes
=======================


[03.01.01] Sigma indexes
========================

[WR./SAVE//ndb.kindx]-----------------------------------------------------------
Fragmentation : no
Polarization last K : 14
QP states : 1 14
X grid is uniform : yes
Grids : X B S
BS scattering : yes
COLL scattering : no
Sigma scattering : yes
X scattering : yes
- S/N 003471 ---------------------------------------------- v.05.00.01 r.19550 -

[04] Dipoles
============

[RD./SAVE//ndb.dipoles]---------------------------------------------------------
Brillouin Zone Q/K grids (IBZ/BZ) : 14 72 14 72
RL vectors : 1491 [WF]
Fragmentation : yes
Electronic Temperature : 0.000000 [K]
Bosonic Temperature : 0.000000 [K]
DIP band range : 1 100
DIP band range limits : 8 9
DIP e/h energy range : -1.000000 -1.000000 [eV]
RL vectors in the sum : 1491
[r,Vnl] included : yes
Bands ordered : yes
Direct v evaluation : no
Approach used : G-space v
Dipoles computed : R V P
Wavefunctions : Slater exchange(X)+Perdew & Zunger(C)
- S/N 003471 ---------------------------------------------- v.05.00.01 r.19550 -

[WARNING] Only commutator with non-local pseudopotential contribution included in position and velocity dipol

[05] Bethe Salpeter Equation @q1
================================


[05.01] Transition Groups build-up @q1
======================================

[BSK] Transition groups (total): 14
[BSK] Size (resonant): 432
[BSK] (total): 432
[BSK] Matricies : 1

[05.02] Independent Particles properties @q1
============================================

[RD./SAVE//ndb.dipoles]---------------------------------------------------------
Jagjit Kaur
Harish-Chandra Research Institute
Allahabad
India

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Error in BSE calculation

Post by Daniele Varsano » Mon Apr 19, 2021 9:56 am

Dear Jagjit,
did you use the database of the tutorial, or they are newly generated?
It seems there are problems in reading the screening previously calculated.
1) Check that the screening calculation was successfully terminated
2) Other ways to proceed to have all consistent:
*remove the ndb.em1s* files from the 3D_BSE directory
*generate a combined input file for screening and BSE kernel

Code: Select all

 yambo -X s -o b -k sex -F 02_3D_BSE_kernel.in -J 3D_BSE
change the variable accordingly to the tutorial being sure to assign the same block in BSENGBlk and NGsBlkXs

Report here if you still have problems.
Please try to attach input/report file using the attachment button, in order to upload them you need to rename them with an allowed suffix (e.g. .txt, .zip)

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

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