I am trying to calculate the non-linear optical constants for a defect in diamond. I generated the input file based upon the tutorial (nonlinear - abinit) based upon the PEAD method. Unfortunately after running for five days, the job failed due to what the code reports as a bug. I have pasted the input file below as well as the last part of the log file reporting the error. Does anyone have any idea as to what an appropriate action would be to get the code to work?
...
kpt: | kpt:
0.1250000 0.1250000 0.1250000 | 0.1250000 0.1250000 0.1250000
0.3750000 0.1250000 0.1250000 | 0.3750000 0.1250000 0.1250000
-0.3750000 0.1250000 0.1250000 | -0.3750000 0.1250000 0.1250000
-0.1250000 0.1250000 0.1250000 | -0.1250000 0.1250000 0.1250000
0.1250000 0.3750000 0.1250000 | 0.1250000 0.3750000 0.1250000
wtk: | wtk:
0.016 0.016 0.016 0.016 0.016 | 0.016 0.016 0.016 0.016 0.016
occ: | occ:
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 | 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 | 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 | 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 | 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 | 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
tnons: | tnons:
0.0000000 0.0000000 0.0000000 | 0.0000000 0.0000000 0.0000000
0.2500000 0.2500000 0.0000000 | 0.2500000 0.2500000 0.0000000
0.2500000 0.2500000 0.0000000 | 0.2500000 0.2500000 0.0000000
0.0000000 0.2500000 -0.2500000 | 0.0000000 0.2500000 -0.2500000
0.0000000 0.2500000 -0.2500000 | 0.0000000 0.2500000 -0.2500000
0.0000000 0.0000000 0.0000000 | 0.0000000 0.0000000 0.0000000
znucl: | znucl:
6.00 7.00 | 6.00 7.00
pseudopotential atom type 1: | pseudopotential atom type 1:
pspso 0 pspxc 11 | pspso 0 pspxc 11
pspdat 150711 pspcod 8 zion 4.0 | pspdat 150711 pspcod 8 zion 4.0
pseudopotential atom type 2: | pseudopotential atom type 2:
pspso 0 pspxc 11 | pspso 0 pspxc 11
pspdat 150713 pspcod 8 zion 5.0 | pspdat 150713 pspcod 8 zion 5.0
xred: | xred:
-0.0000817 0.9991255 1.0000817 | -0.0000817 0.9991255 1.0000817
-0.0000184 0.0005250 0.5001061 | -0.0000184 0.0005250 0.5001061
0.0016379 0.4991954 0.9983621 | 0.0016379 0.4991954 0.9983621
0.9978087 0.5008869 0.4973330 | 0.9978087 0.5008869 0.4973330
0.4998939 0.0005250 1.0000184 | 0.4998939 0.0005250 1.0000184
0.4998172 0.0007132 0.5001828 | 0.4998172 0.0007132 0.5001828
0.5026670 0.5008869 0.0021913 | 0.5026670 0.5008869 0.0021913
0.4900396 0.4951613 0.5099604 | 0.4900396 0.4951613 0.5099604
0.3777663 0.3785896 0.3750992 | 0.3777663 0.3785896 0.3750992
0.3761215 0.3754361 0.8759010 | 0.3761215 0.3754361 0.8759010
0.3752321 0.8747679 0.3755614 | 0.3752321 0.8747679 0.3755614
0.3749929 0.8750071 0.8755931 | 0.3749929 0.8750071 0.8755931
0.8749416 0.3750584 0.3687393 | 0.8749416 0.3750584 0.3687393
0.8753011 0.3746989 0.8735954 | 0.8753011 0.3746989 0.8735954
0.8714104 0.8722337 0.3750992 | 0.8714104 0.8722337 0.3750992
0.8745639 0.8738785 0.8759010 | 0.8745639 0.8738785 0.8759010
0.3761215 0.1259010 0.1254361 | 0.3761215 0.1259010 0.1254361
0.3749929 0.1255931 0.6250071 | 0.3749929 0.1255931 0.6250071
0.3777663 0.6250992 0.1285896 | 0.3777663 0.6250992 0.1285896
0.3752321 0.6255614 0.6247679 | 0.3752321 0.6255614 0.6247679
0.8753011 0.1235954 0.1246989 | 0.8753011 0.1235954 0.1246989
0.8745639 0.1259010 0.6238785 | 0.8745639 0.1259010 0.6238785
0.8749416 0.6187393 0.1250584 | 0.8749416 0.6187393 0.1250584
0.8714104 0.6250992 0.6222337 | 0.8714104 0.6250992 0.6222337
0.1264046 0.3746989 0.1246989 | 0.1264046 0.3746989 0.1246989
0.1240990 0.3754361 0.6238785 | 0.1240990 0.3754361 0.6238785
0.1240990 0.8738785 0.1254361 | 0.1240990 0.8738785 0.1254361
0.1244069 0.8750071 0.6250071 | 0.1244069 0.8750071 0.6250071
0.6312607 0.3750584 0.1250584 | 0.6312607 0.3750584 0.1250584
0.6249008 0.3785896 0.6222337 | 0.6249008 0.3785896 0.6222337
0.6249008 0.8722337 0.1285896 | 0.6249008 0.8722337 0.1285896
0.6244386 0.8747679 0.6247679 | 0.6244386 0.8747679 0.6247679
0.1250995 0.1249005 0.3746492 | 0.1250995 0.1249005 0.3746492
0.1251493 0.1248507 0.8748507 | 0.1251493 0.1248507 0.8748507
0.1247303 0.6250694 0.3750694 | 0.1247303 0.6250694 0.3750694
0.1250995 0.6246492 0.8749005 | 0.1250995 0.6246492 0.8749005
0.6249306 0.1252697 0.3750694 | 0.6249306 0.1252697 0.3750694
0.6253508 0.1249005 0.8749005 | 0.6253508 0.1249005 0.8749005
0.6249306 0.6250694 0.8752697 | 0.6249306 0.6250694 0.8752697
0.0016379 0.2483621 0.2491954 | 0.0016379 0.2483621 0.2491954
0.9999183 0.2500817 0.7491255 | 0.9999183 0.2500817 0.7491255
0.9978087 0.7473330 0.2508869 | 0.9978087 0.7473330 0.2508869
0.9999816 0.7501061 0.7505250 | 0.9999816 0.7501061 0.7505250
0.5026670 0.2521913 0.2508869 | 0.5026670 0.2521913 0.2508869
0.4998939 0.2500184 0.7505250 | 0.4998939 0.2500184 0.7505250
0.4900396 0.7599604 0.2451613 | 0.4900396 0.7599604 0.2451613
0.4998172 0.7501828 0.7507132 | 0.4998172 0.7501828 0.7507132
0.2508745 0.2500817 0.0000817 | 0.2508745 0.2500817 0.0000817
0.2494750 0.2500184 0.5001061 | 0.2494750 0.2500184 0.5001061
0.2494750 0.7501061 0.0000184 | 0.2494750 0.7501061 0.0000184
0.2492868 0.7501828 0.5001828 | 0.2492868 0.7501828 0.5001828
0.7508046 0.2483621 0.9983621 | 0.7508046 0.2483621 0.9983621
0.7491131 0.2521913 0.4973330 | 0.7491131 0.2521913 0.4973330
0.7491131 0.7473330 0.0021913 | 0.7491131 0.7473330 0.0021913
0.7548387 0.7599604 0.5099604 | 0.7548387 0.7599604 0.5099604
0.2489344 0.0010656 0.2503311 | 0.2489344 0.0010656 0.2503311
0.2498738 1.0001262 0.7501262 | 0.2498738 1.0001262 0.7501262
0.2506585 0.5004523 0.2504523 | 0.2506585 0.5004523 0.2504523
0.2489344 0.5003311 0.7510656 | 0.2489344 0.5003311 0.7510656
0.7495477 -0.0006585 0.2504523 | 0.7495477 -0.0006585 0.2504523
0.7496689 0.0010656 0.7510656 | 0.7496689 0.0010656 0.7510656
0.7495477 0.5004523 0.7493415 | 0.7495477 0.5004523 0.7493415
0.7608648 0.4891352 0.2391352 | 0.7608648 0.4891352 0.2391352
hdr_check: Wavefunction file is OK for direct restart of calculation
================================================================================
-inwffil : will read wavefunctions from disk file outdata/outnc_DS2_WFK
initwf: disk file gives npw= 40636 nband= 127 for kpt number= 1
initwf: 127 bands have been initialized from disk
respfn : eigen0 array
mkrho: echo density (plane-wave part only)
Total charge density [el/Bohr^3]
Maximum= 6.7836E-01 at reduced coord. 0.7333 0.5111 0.2667
Minimum= 1.0852E-02 at reduced coord. 0.7333 0.7222 0.2667
Integrated= 2.5300E+02
max_dist 9.944610103386904E-002
Neighbors(1:ishell,1) 6
Weights (1:ishell) 1448.02057097201
1448.02057097201 1448.02057097201 1448.02057097201
1448.02057097201 1448.02057097201 1448.02057097201
getshell: BUG -
The calculated weights do not solve the linear system for all k-points.
max_err: 1.99970065E-05 > tolerance: 5.00000000E-06
getshell: BUG -
The calculated weights do not solve the linear system for all k-points.
max_err: 1.99970065E-05 > tolerance: 5.00000000E-06
Action: contact ABINIT group (please attach the output of `abinit -b`)
Action: contact ABINIT group (please attach the output of `abinit -b`)
--- !BUG
src_file: m_getshell.F90
src_line: 673
mpi_rank: 0
message: |
There is a problem with the finite difference expression of the ddk
If you are very close to a symmetric structure, you might be confusing the algorithm with
sets of k-points which are not quite part of the same shell. Try rectifying angles and acell.
...
Abort(13) on node 37 (rank 37 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 13) - process 37
ndtset 5
#### Global Variables.
############################################################################################
ngkpt 4 4 4
nshiftk 1
shiftk 0.5 0.5 0.5
ecut 45
occopt 1
nstep 200
optdriver 0
nsppol 1
dilatmx 1.05
ecutsm 0.5
nband 127
nbdbuf 0
# suppress printing of density, wavefunctions, etc except what is
# # explicitly requested above in the ndtset section
prtwf 0
prtden 0
prteig 0
indata_prefix "indata/in"
tmpdata_prefix "tmpdata/tmp"
outdata_prefix "outdata/outnc"
pp_dirpath "/data/abinit/pseudos"
pseudos
"C_LDA.psp8,
N_LDA.psp8"
############################################################################################
#### STRUCTURE
############################################################################################
natom 63
ntypat 2
typat
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 1
1 1 2
znucl 6 7
xred
-8.1727793557d-05 0.9991255085 1.0000817278
-1.8435613594d-05 5.2501921200d-04 0.5001060909
0.0016378679 0.4991954111 0.9983621321
0.9978086865 0.5008868602 0.4973330238
0.4998939091 5.2501921200d-04 1.0000184356
0.4998171893 7.1321590155d-04 0.5001828107
0.5026669762 0.5008868602 0.0021913135
0.4900396379 0.4951612619 0.5099603621
0.3777663362 0.3785896418 0.3750992211
0.3761215446 0.3754360679 0.8759010340
0.3752321248 0.8747678752 0.3755613916
0.3749928802 0.8750071198 0.8755930508
0.8749416146 0.3750583854 0.3687393417
0.8753010584 0.3746989416 0.8735954097
0.8714103582 0.8722336638 0.3750992211
0.8745639321 0.8738784554 0.8759010340
0.3761215446 0.1259010340 0.1254360679
0.3749928802 0.1255930508 0.6250071198
0.3777663362 0.6250992211 0.1285896418
0.3752321248 0.6255613916 0.6247678752
0.8753010584 0.1235954097 0.1246989416
0.8745639321 0.1259010340 0.6238784554
0.8749416146 0.6187393417 0.1250583854
0.8714103582 0.6250992211 0.6222336638
0.1264045903 0.3746989416 0.1246989416
0.1240989660 0.3754360679 0.6238784554
0.1240989660 0.8738784554 0.1254360679
0.1244069492 0.8750071198 0.6250071198
0.6312606583 0.3750583854 0.1250583854
0.6249007789 0.3785896418 0.6222336638
0.6249007789 0.8722336638 0.1285896418
0.6244386084 0.8747678752 0.6247678752
0.1250994533 0.1249005467 0.3746491815
0.1251492983 0.1248507017 0.8748507017
0.1247303250 0.6250693536 0.3750693536
0.1250994533 0.6246491815 0.8749005467
0.6249306464 0.1252696750 0.3750693536
0.6253508185 0.1249005467 0.8749005467
0.6249306464 0.6250693536 0.8752696750
0.0016378679 0.2483621321 0.2491954111
0.9999182722 0.2500817278 0.7491255085
0.9978086865 0.7473330238 0.2508868602
0.9999815644 0.7501060909 0.7505250192
0.5026669762 0.2521913135 0.2508868602
0.4998939091 0.2500184356 0.7505250192
0.4900396379 0.7599603621 0.2451612619
0.4998171893 0.7501828107 0.7507132159
0.2508744915 0.2500817278 8.1727793557d-05
0.2494749808 0.2500184356 0.5001060909
0.2494749808 0.7501060909 1.8435613594d-05
0.2492867841 0.7501828107 0.5001828107
0.7508045889 0.2483621321 0.9983621321
0.7491131398 0.2521913135 0.4973330238
0.7491131398 0.7473330238 0.0021913135
0.7548387381 0.7599603621 0.5099603621
0.2489344108 0.0010655892 0.2503311004
0.2498738311 1.0001261689 0.7501261689
0.2506584627 0.5004522646 0.2504522646
0.2489344108 0.5003311004 0.7510655892
0.7495477354 -6.5846272032d-04 0.2504522646
0.7496688996 0.0010655892 0.7510655892
0.7495477354 0.5004522646 0.7493415373
0.7608648352 0.4891351648 0.2391351648
acell 1.0 1.0 1.0
rprim
13.4537196110 2.4577523146d-06 -8.7490491474d-07
-9.7139789812d-07 13.4537196110 -1.2410041145d-05
2.3612581455d-06 1.0923686090d-05 13.4537196110
#####################
##### DATASET 1 #####
#####################
##############################################
#### SECTION: basic
##############################################
kptopt1 3
toldfe1 1e-12
##############################################
#### SECTION: files
##############################################
prtden1 1
prtwf1 1
##############################################
#### SECTION: paral
##############################################
autoparal1 1
#####################
##### DATASET 2 #####
#####################
##############################################
#### SECTION: basic
##############################################
kptopt2 3
iscf2 -2
tolwfr2 1e-22
##############################################
#### SECTION: files
##############################################
getden2 1
getwfk2 1
prtwf2 1
##############################################
#### SECTION: paral
##############################################
autoparal2 1
#####################
##### DATASET 3 #####
#####################
##############################################
#### SECTION: basic
##############################################
kptopt3 3
tolwfr3 1e-22
##############################################
#### SECTION: dfpt
##############################################
optdriver3 1
rfelfd3 2
##############################################
#### SECTION: files
##############################################
getwfk3 2
prtwf3 1
#####################
##### DATASET 4 #####
#####################
##############################################
#### SECTION: basic
##############################################
kptopt4 3
tolvrs4 1e-12
##############################################
#### SECTION: dfpt
##############################################
optdriver4 1
rfphon4 1
rfelfd4 3
rfstrs4 3
prepanl4 1
##############################################
#### SECTION: files
##############################################
getwfk4 2
getddk4 3
prtwf4 1
prtden4 1
#####################
##### DATASET 5 #####
#####################
##############################################
#### SECTION: basic
##############################################
kptopt5 3
##############################################
#### SECTION: dfpt
##############################################
optdriver5 5
d3e_pert1_elfd5 1 # activate electric field for 1st perturbation...
d3e_pert1_phon5 1 # ...and also atomic displacements...
d3e_pert1_atpol5 1 63 # ...for all atoms
d3e_pert2_elfd5 1 # activate electric field for 2nd perturbation...
d3e_pert3_elfd5 1 # activate electric field for 3rd perturbation...
##############################################
#### SECTION: files
##############################################
getwfk5 2
get1den5 4
get1wf5 4
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-015
Smallest positive number: 0.22250739E-307
Largest representable number: 0.17976931E+309
INTEGER: Data type name: INTEGER(default)
Kind value: 4
Bit size: 32
Largest representable number: 2147483647
LOGICAL: Data type name: LOGICAL
Kind value: 4
CHARACTER: Data type name: CHARACTER Kind value: 1
==== Using MPI-2 specifications ====
MPI-IO support is ON
xmpi_tag_ub ................ 1048575
xmpi_bsize_ch .............. 1
xmpi_bsize_int ............. 4
xmpi_bsize_sp .............. 4
xmpi_bsize_dp .............. 8
xmpi_bsize_spc ............. 8
xmpi_bsize_dpc ............. 16
xmpio_bsize_frm ............ 4
xmpi_address_kind .......... 8
xmpi_offset_kind ........... 8
MPI_WTICK .................. 4.358080898341752E-010
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:
CC_INTEL CXX_GNU FC_INTEL
HAVE_DFTI HAVE_FC_ALLOCATABLE_DT... HAVE_FC_ASYNC
HAVE_FC_COMMAND_ARGUMENT HAVE_FC_COMMAND_LINE HAVE_FC_CONTIGUOUS
HAVE_FC_CPUTIME HAVE_FC_ETIME HAVE_FC_EXIT
HAVE_FC_FLUSH HAVE_FC_GAMMA HAVE_FC_GETENV
HAVE_FC_GETPID HAVE_FC_IEEE_ARITHMETIC HAVE_FC_IEEE_EXCEPTIONS
HAVE_FC_IOMSG HAVE_FC_ISO_C_BINDING HAVE_FC_ISO_FORTRAN_2008
HAVE_FC_LONG_LINES HAVE_FC_MOVE_ALLOC HAVE_FC_ON_THE_FLY_SHAPE
HAVE_FC_PRIVATE HAVE_FC_PROTECTED HAVE_FC_SHIFTLR
HAVE_FC_STREAM_IO HAVE_FC_SYSTEM HAVE_GW_DPC
HAVE_HDF5 HAVE_HDF5_MPI HAVE_LIBPAW_ABINIT
HAVE_LIBTETRA_ABINIT HAVE_LIBXC HAVE_LINALG_AXPBY
HAVE_LINALG_GEMM3M HAVE_LINALG_GEMMT HAVE_LINALG_MKL_IMATCOPY
HAVE_LINALG_MKL_OMATADD HAVE_LINALG_MKL_OMATCOPY HAVE_LINALG_MKL_THREADS
HAVE_LINALG_SCALAPACK HAVE_MPI HAVE_MPI2
HAVE_MPI_IALLGATHER HAVE_MPI_IALLREDUCE HAVE_MPI_IALLTOALL
HAVE_MPI_IALLTOALLV HAVE_MPI_IBCAST HAVE_MPI_IGATHERV
HAVE_MPI_INTEGER16 HAVE_MPI_IO HAVE_MPI_TYPE_CREATE_S...
HAVE_NETCDF HAVE_NETCDF_FORTRAN HAVE_NETCDF_FORTRAN_MPI
HAVE_NETCDF_MPI HAVE_NUMPY HAVE_OMP_COLLAPSE
HAVE_OPENMP HAVE_OS_LINUX HAVE_TIMER_ABINIT
HAVE_WANNIER90
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=== Build Information ===
Version : 9.6.2
Build target : x86_64_linux_intel2021.6
Build date : 20230712
=== Compiler Suite ===
C compiler : intel2021.6
C++ compiler : gnu2021.6
Fortran compiler : intel2021.6
CFLAGS : -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fopenmp -fPIC -mt_mpi
CXXFLAGS : -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fopenmp -fPIC -mt_mpi
FCFLAGS : -O2 -xHost -ftz -fp-speculation=safe -fp-model source -fopenmp -fPI ...
FC_LDFLAGS : -static-intel -static-libgcc
=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : intel_xeon
=== Multicore ===
Parallel build : yes
Parallel I/O :
openMP support : yes
GPU support :
=== Connectors / Fallbacks ===
LINALG flavor : mkl
FFT flavor : dfti
HDF5 : yes
NetCDF : yes
NetCDF Fortran : yes
LibXC : yes
Wannier90 : yes
=== Experimental features ===
Exports :
GW double-precision : yes
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
--- None ---