Dear Eric,
with further calculation I meant, that it finds the correct symmetry, but that it cannot calculate the energy. E.G. from the end of my logfile
Code: Select all
Number of q-points for radial functions ffspl .. 3001
Number of q-points for vlspl ................... 3001
vloc is computed in Reciprocal Space
model core charge treated in real-space
XC functional for type 1 is 1
Pseudo valence available: no
wfconv: 8 bands initialized randomly with npw= 62, for ikpt= 1
_setup2: Arith. and geom. avg. npw (full set) are 62.750 62.748
initro: for itypat= 1, take decay length= 0.8000,
initro: indeed, coreel= 54.0000, nval= 16 and densty= 0.0000E+00.
================================================================================
getcut: wavevector= 0.0000 0.0000 0.0000 ngfft= 20 20 20
ecut(hartree)= 8.000 => boxcut(ratio)= 2.22144
getcut : COMMENT -
Note that boxcut > 2.2 ; recall that boxcut=Gcut(box)/Gcut(sphere) = 2
is sufficient for exact treatment of convolution.
Such a large boxcut is a waste : you could raise ecut
e.g. ecut= 9.869604 Hartrees makes boxcut=2
Job /opt/lsf/10.1/linux2.6-glibc2.3-x86_64/bin/intelmpi_wrapper ./abinit
TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME
===== ========== ================ ======================= ===================
00000 gwdc061 ./abinit Exit (174) 04/20/2018 16:34:58
00001 gwdc061 ./abinit Exit (status unknown)
00002 gwdc061 ./abinit Exit (status unknown)
00003 gwdc061 ./abinit Exit (status unknown)
00004 gwdc061 ./abinit Exit (status unknown)
00005 gwdc061 ./abinit Exit (status unknown)
00006 gwdc061 ./abinit Exit (status unknown)
00007 gwdc061 ./abinit Exit (174) 04/20/2018 16:34:58
However, it seems that my problem now could be solved together with the help of our cluster admins.
I give now my configuration file:
Code: Select all
#destination of executables
prefix="/usr/users/hgibhar/abinit-8.6.3.parallel/myabinitparallel"
FC=mpiifort
F77=mpiifort
F90=mpiifort
CC=mpiicc
CXX=mpiicpc
FCFLAGS="-O2 -mkl -fp-model precise"
FFLAGS="-O2 -mkl -fp-model precise"
CFLAGS="-O2 -mkl -fp-model precise"
CXXFLAGS="-O2 -mkl -fp-model precise"
enable_mpi = 'yes'
enable_mpi_inplace='yes'
enable_zdot_bugfix='yes'
enable_avx_safe_mode='yes'
enable_fallbacks='yes'
#################
CPPFLAGS="-I${MKLROOT}/include -I${MKLROOT}/include/fftw"
LDFLAGS="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm"
##############
with_trio_flavor='netcdf'
with_linalg_flavor='mkl'
with_dft_flavor='atompaw+bigdft+libxc'
enable_gw_dpc='yes'
enable_maintainer_checks='no'
With this file, the modules
Code: Select all
module load intel/compiler/64
module load intel/mpi/64
module load intel/mkl/64
but without
now, I can run the example test_v1 also as parallel run with mpi and it calculates the same as with a sequential run.
The end of the logfile is
Code: Select all
XC functional for type 1 is 1
Pseudo valence available: no
wfconv: 8 bands initialized randomly with npw= 16, for ikpt= 1
wfconv: 8 bands initialized randomly with npw= 16, for ikpt= 2
_setup2: Arith. and geom. avg. npw (full set) are 16.000 16.000
initro: for itypat= 1, take decay length= 0.8000,
initro: indeed, coreel= 54.0000, nval= 16 and densty= 0.0000E+00.
================================================================================
getcut: wavevector= 0.0000 0.0000 0.0000 ngfft= 20 20 20
ecut(hartree)= 8.000 => boxcut(ratio)= 2.22144
getcut : COMMENT -
Note that boxcut > 2.2 ; recall that boxcut=Gcut(box)/Gcut(sphere) = 2
is sufficient for exact treatment of convolution.
Such a large boxcut is a waste : you could raise ecut
e.g. ecut= 9.869604 Hartrees makes boxcut=2
ITER STEP NUMBER 1
vtorho : nnsclo_now=2, note that nnsclo,dbl_nnsclo,istep=0 0 1
- Will use non-blocking ialltoall for MPI-FFT
--- !WARNING
src_file: vtorho.F90
src_line: 1585
message: |
For k-point number 1,
The minimal occupation factor is 2.000.
An adequate monitoring of convergence requires it to be at most 0.01_dp.
Action: increase slightly the number of bands.
...
Total charge density [el/Bohr^3]
Maximum= 4.5633E-01 at reduced coord. 0.0500 0.8500 0.2000
Minimum= 5.8762E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 1 -69.636426934385 -6.964E+01 1.025E-04 1.158E+01
scprqt: <Vxc>= -3.7631157E-01 hartree
Simple mixing update:
residual square of the potential : 5.39325405079883
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 2
vtorho : nnsclo_now=2, note that nnsclo,dbl_nnsclo,istep=0 0 2
--- !WARNING
src_file: vtorho.F90
src_line: 1585
message: |
For k-point number 1,
The minimal occupation factor is 2.000.
An adequate monitoring of convergence requires it to be at most 0.01_dp.
Action: increase slightly the number of bands.
...
Total charge density [el/Bohr^3]
Maximum= 4.8571E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8067E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 2 -69.657561749079 -2.113E-02 4.227E-04 2.727E-01
scprqt: <Vxc>= -3.7516948E-01 hartree
Pulay update with 1 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 0.994 0.572E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 3
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 3
--- !WARNING
src_file: vtorho.F90
src_line: 1585
message: |
For k-point number 1,
The minimal occupation factor is 2.000.
An adequate monitoring of convergence requires it to be at most 0.01_dp.
Action: increase slightly the number of bands.
...
Total charge density [el/Bohr^3]
Maximum= 4.9082E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.9121E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 3 -69.662710097185 -5.148E-03 2.953E-04 1.753E-01
scprqt: <Vxc>= -3.7710077E-01 hartree
Pulay update with 2 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 0.685 0.349 -0.345E-01
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 4
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 4
--- !WARNING
src_file: vtorho.F90
src_line: 1585
message: |
For k-point number 1,
The minimal occupation factor is 2.000.
An adequate monitoring of convergence requires it to be at most 0.01_dp.
Action: increase slightly the number of bands.
...
Total charge density [el/Bohr^3]
Maximum= 4.9236E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8827E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 4 -69.663968164086 -1.258E-03 1.333E-05 9.465E-03
scprqt: <Vxc>= -3.7667317E-01 hartree
Pulay update with 3 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.46 -0.412 -0.576E-01 0.886E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 5
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 5
--- !WARNING
src_file: vtorho.F90
src_line: 1585
message: |
For k-point number 1,
The minimal occupation factor is 2.000.
An adequate monitoring of convergence requires it to be at most 0.01_dp.
Action: increase slightly the number of bands.
...
Total charge density [el/Bohr^3]
Maximum= 4.9240E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8691E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 5 -69.664154395287 -1.862E-04 1.148E-05 9.470E-04
scprqt: <Vxc>= -3.7664246E-01 hartree
Pulay update with 4 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.07 -0.618E-01 -0.313E-01 0.249E-01 -0.131E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 6
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 6
Total charge density [el/Bohr^3]
Maximum= 4.9253E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8596E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 6 -69.664208611081 -5.422E-05 9.153E-07 1.030E-04
scprqt: <Vxc>= -3.7661878E-01 hartree
Pulay update with 5 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.31 -0.261 -0.564E-01 0.322E-02 0.371E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 7
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 7
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8572E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 7 -69.664223749490 -1.514E-05 8.222E-07 1.073E-05
scprqt: <Vxc>= -3.7661573E-01 hartree
Pulay update with 6 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.07 0.711E-01 -0.124 -0.153E-01 0.149E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 8
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 8
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8555E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 8 -69.664228584369 -4.835E-06 9.034E-08 1.594E-06
scprqt: <Vxc>= -3.7660864E-01 hartree
Pulay update with 7 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 0.865 0.136 -0.766E-02 0.793E-02 -0.431E-02
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 9
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 9
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8557E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 9 -69.664230057412 -1.473E-06 7.008E-08 6.763E-08
scprqt: <Vxc>= -3.7660998E-01 hartree
Pulay update with 7 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.02 -0.481E-02 -0.406E-01 0.269E-01 0.637E-04
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 10
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 10
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8557E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 10 -69.664230547932 -4.905E-07 9.008E-09 5.006E-08
scprqt: <Vxc>= -3.7660959E-01 hartree
Pulay update with 7 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 0.883 0.150 -0.495E-01 0.240E-01 -0.158E-01
scfcv: previous iteration took 00 [s]
ITER STEP NUMBER 11
vtorho : nnsclo_now=1, note that nnsclo,dbl_nnsclo,istep=0 0 11
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Minimum= 5.8558E-03 at reduced coord. 0.5000 0.5000 0.0000
Integrated= 1.6000E+01
ETOT 11 -69.664230709087 -1.612E-07 6.983E-09 2.272E-09
scprqt: <Vxc>= -3.7660987E-01 hartree
Pulay update with 7 previous iterations:
mixing of old trial potential : alpha(m:m-4)= 1.04 -0.192E-01 -0.125 0.774E-01 0.318E-01
Computing residual forces using gaussian functions as atomic densities
Cartesian components of stress tensor (hartree/bohr^3)
sigma(1 1)= 8.13993553E-03 sigma(3 2)= 0.00000000E+00
sigma(2 2)= 8.13993553E-03 sigma(3 1)= 0.00000000E+00
sigma(3 3)= 8.13993553E-03 sigma(2 1)= 0.00000000E+00
--- !ScfConvergenceWarning
message: |
nstep 11 was not enough SCF cycles to converge.
...
scprqt: WARNING -
nstep= 11 was not enough SCF cycles to converge;
maximum residual each band. tolwfr= 1.000E-14
iband, isppol, individual band residuals (max over all k-points):
1 1 2.229E-17
2 1 8.188E-18
3 1 7.116E-18
4 1 8.328E-18
5 1 6.595E-18
6 1 5.285E-18
7 1 2.659E-17
8 1 6.983E-09
maximum residual= 6.983E-09 exceeds tolwfr= 1.000E-14
fftdatar_write: About to write data to: testin_v1_o_DEN with iomode IO_MODE_MPI
IO operation completed. cpu_time: 0.0 [s], walltime: 0.0 [s]
================================================================================
----iterations are completed or convergence reached----
=== Gap info ===
Not enough states to calculate the band gap.
Mean square residual over all n,k,spin= 4.3642E-10; max= 6.9827E-09
0.2500 0.2500 0.2500 1 6.98267E-09 kpt; spin; max resid(k); each band:
1.19E-17 8.19E-18 7.12E-18 8.33E-18 5.38E-18 4.68E-18 2.66E-17 6.98E-09
0.2500 0.5000 0.5000 1 3.13998E-15 kpt; spin; max resid(k); each band:
2.23E-17 5.58E-18 4.44E-18 5.57E-18 6.60E-18 5.28E-18 2.22E-17 3.14E-15
outwf: write wavefunction to file testin_v1_o_WFK, with iomode 1
outwf with iomode: 1, cpu_time: 0.01[s], walltime: 0.12 [s]
prteigrs : about to open file testin_v1_o_EIG
Fermi (or HOMO) energy (hartree) = 0.06514 Average Vxc (hartree)= -0.37661
Eigenvalues (hartree) for nkpt= 2 k points:
kpt# 1, nband= 8, wtk= 0.25000, kpt= 0.2500 0.2500 0.2500 (reduced coord)
-0.76380 -0.68036 -0.67729 -0.67729 -0.67116 -0.67116 -0.16331 0.06514
kpt# 2, nband= 8, wtk= 0.75000, kpt= 0.2500 0.5000 0.5000 (reduced coord)
-0.75775 -0.68699 -0.67328 -0.66901 -0.66186 -0.65563 -0.12682 -0.03042
Fermi (or HOMO) energy (eV) = 1.77260 Average Vxc (eV)= -10.24808
Eigenvalues ( eV ) for nkpt= 2 k points:
kpt# 1, nband= 8, wtk= 0.25000, kpt= 0.2500 0.2500 0.2500 (reduced coord)
-20.78414 -18.51364 -18.43011 -18.43011 -18.26329 -18.26329 -4.44382 1.77260
kpt# 2, nband= 8, wtk= 0.75000, kpt= 0.2500 0.5000 0.5000 (reduced coord)
-20.61956 -18.69386 -18.32082 -18.20481 -18.01022 -17.84052 -3.45108 -0.82789
Total charge density [el/Bohr^3]
Maximum= 4.9256E-01 at reduced coord. 0.0000 0.0000 0.0000
Next maximum= 4.6364E-01 at reduced coord. 0.0500 0.8500 0.2000
Minimum= 5.8558E-03 at reduced coord. 0.5000 0.5000 0.0000
Next minimum= 6.1049E-03 at reduced coord. 0.5000 0.5000 0.2000
Integrated= 1.6000E+01
Cartesian components of stress tensor (hartree/bohr^3)
sigma(1 1)= 8.13993553E-03 sigma(3 2)= 0.00000000E+00
sigma(2 2)= 8.13993553E-03 sigma(3 1)= 0.00000000E+00
sigma(3 3)= 8.13993553E-03 sigma(2 1)= 0.00000000E+00
-Cartesian components of stress tensor (GPa) [Pressure= -2.3949E+02 GPa]
- sigma(1 1)= 2.39485131E+02 sigma(3 2)= 0.00000000E+00
- sigma(2 2)= 2.39485131E+02 sigma(3 1)= 0.00000000E+00
- sigma(3 3)= 2.39485131E+02 sigma(2 1)= 0.00000000E+00
== END DATASET(S) ==============================================================
================================================================================
-outvars: echo values of variables after computation --------
These variables are accessible in NetCDF format (testin_v1_o_OUT.nc)
- iomode 1
acell 1.0000000000E+01 1.0000000000E+01 1.0000000000E+01 Bohr
amu 1.73040000E+02
autoparal 1
bandpp 2
chkexit 2
densfor_pred 6
dielng 8.00000000E-01 Bohr
ecut 8.00000000E+00 Hartree
enunit 2
etotal -6.9664230709E+01
fcart 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
- fftalg 401
intxc 1
kpt 1.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 2.00000000E+00 2.00000000E+00
kptnrm 4.00000000E+00
kptopt 0
P mkmem 2
natom 1
nband 8
ngfft 20 20 20
nkpt 2
nline 3
- npband 4
- npfft 4
nstep 11
nsym 24
ntypat 1
occ 2.000000 2.000000 2.000000 2.000000 2.000000 2.000000
2.000000 2.000000
occopt 0
ortalg -2
paral_kgb 1
prtvol 1
rprim 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01
5.0000000000E-01 0.0000000000E+00 5.0000000000E-01
5.0000000000E-01 5.0000000000E-01 0.0000000000E+00
spgroup 216
strten 8.1399355275E-03 8.1399355275E-03 8.1399355275E-03
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
symrel 1 0 0 0 1 0 0 0 1 0 1 -1 1 0 -1 0 0 -1
0 -1 1 0 -1 0 1 -1 0 -1 0 0 -1 0 1 -1 1 0
0 1 0 0 0 1 1 0 0 1 0 -1 0 0 -1 0 1 -1
0 -1 0 1 -1 0 0 -1 1 -1 0 1 -1 1 0 -1 0 0
0 0 1 1 0 0 0 1 0 0 0 -1 0 1 -1 1 0 -1
1 -1 0 0 -1 1 0 -1 0 -1 1 0 -1 0 0 -1 0 1
1 0 -1 0 1 -1 0 0 -1 0 1 0 1 0 0 0 0 1
-1 0 1 -1 0 0 -1 1 0 0 -1 0 0 -1 1 1 -1 0
-1 1 0 -1 0 1 -1 0 0 1 -1 0 0 -1 0 0 -1 1
0 0 -1 1 0 -1 0 1 -1 0 0 1 0 1 0 1 0 0
0 -1 1 1 -1 0 0 -1 0 -1 0 0 -1 1 0 -1 0 1
1 0 0 0 0 1 0 1 0 0 1 -1 0 0 -1 1 0 -1
tolwfr 1.00000000E-14
typat 1
wfoptalg 114
wtk 0.25000 0.75000
znucl 70.00000
================================================================================
================================================================================
Suggested references for the acknowledgment of ABINIT usage.
.
.
.
Calculation completed.
.Delivered 1 WARNINGs and 2 COMMENTs to log file.
--- !FinalSummary
program: abinit
version: 8.6.3
start_datetime: Mon Apr 23 17:25:25 2018
end_datetime: Mon Apr 23 17:25:29 2018
overall_cpu_time: 54.5
overall_wall_time: 70.0
exit_requested_by_user: no
timelimit: 0
pseudos:
Yb : 56bf3aea2f5a48028cfd174a5aa25641
usepaw: 0
mpi_procs: 16
omp_threads: 1
num_warnings: 1
num_comments: 2
...
Memory Consumption Report:
Tot. No. of Allocations : 0
Tot. No. of Deallocations : 0
Remaining Memory (B) : 0
Memory occupation:
Peak Value (MB) : 0
for the array : null
in the routine : null
Max No. of dictionaries used : 807 #( 797 still in use)
Number of dictionary folders allocated: 1
Job /opt/lsf/10.1/linux2.6-glibc2.3-x86_64/bin/intelmpi_wrapper ./abinit
TID HOST_NAME COMMAND_LINE STATUS TERMINATION_TIME
===== ========== ================ ======================= ===================
00000 dmp056 ./abinit Done 04/23/2018 17:25:30
00001 dmp056 ./abinit Done 04/23/2018 17:25:30
00002 dmp056 ./abinit Done 04/23/2018 17:25:30
00003 dmp056 ./abinit Done 04/23/2018 17:25:30
00004 dmp056 ./abinit Done 04/23/2018 17:25:30
00005 dmp056 ./abinit Done 04/23/2018 17:25:30
00006 dmp056 ./abinit Done 04/23/2018 17:25:30
00007 dmp056 ./abinit Done 04/23/2018 17:25:30
00008 dmp056 ./abinit Done 04/23/2018 17:25:30
00009 dmp056 ./abinit Done 04/23/2018 17:25:30
00010 dmp056 ./abinit Done 04/23/2018 17:25:30
00011 dmp056 ./abinit Done 04/23/2018 17:25:30
00012 dmp056 ./abinit Done 04/23/2018 17:25:30
00013 dmp056 ./abinit Done 04/23/2018 17:25:30
00014 dmp056 ./abinit Done 04/23/2018 17:25:30
00015 dmp056 ./abinit Done 04/23/2018 17:25:30
Let me thank you, Eric, for your help. I mark this now as solved.
Best regards
Holger
