input file foroptimization

[hameed1987]

Dear Sirs
I tried to do optimization for Ge., but it gave below error. I do not know what is inconsistency in my input file.

Please help me to solve the problem. The input file is attached as well as copied after message error.

--- !ERROR
src_file: chkinp.F90
src_line: 3388
mpi_rank: 2
message: |
Checking consistency of input data against itself gave 1 inconsistency.
The details of the problem can be found above.


the input file is

# Germanium : computation of the total energy
#

#Definition of the unit cell
nspinor 2
ionmov 2
optcell 2
ngfft 0 0 0

ecutsm 0.5
dilatmx 1.0
ntime 0
strfact 100
restartxf 0

#commonn inputs
acell 3*5.658 Angstr
rprim 1 0 0
0 1 0
0 0 1

#Definition of the atom types
ntypat 1 # There is only one type of atom
znucl 32 # The keyword "znucl" refers to the atomic number of the
# possible type(s) of atom. The pseudopotential(s)
# mentioned in the "files" file must correspond
# to the type(s) of atom. Here, the only type is Silicon.


#Definition of the atoms
natom 2 # There are two atoms
typat 1 1 # They both are of type 1, that is, Silicon.
xred 0.25 0.25 0.25
0.0 0.0 0.0

#Definition of the planewave basis set
ecut 20


#Definition of the k-point grid
kptopt 1 # Option for the automatic generation of k points, taking
# into account the symmetry
ngkpt 6 6 6
nshiftk 4 # of the reciprocal space (that form a BCC lattice !),
# repeated four times, with different shifts :
shiftk 0.5 0.5 0.5
0.5 0.0 0.0
0.0 0.5 0.0
0.0 0.0 0.5
# In cartesian coordinates, this grid is simple cubic, and
# actually corresponds to the
# so-called 4x4x4 Monkhorst-Pack grid

#Definition of the SCF procedure
nstep 1000
tolrff 0.0
toldff 0.0
tolwfr 0.0
tolmxf 5e-05
toldfe 1.0d-22
tolmxde 0.0
diemac 12.0 # Although this is not mandatory, it is worth to
# precondition the SCF cycle. The model dielectric
# function used as the standard preconditioner

#Definition of Strprecon
strprecon 1.0
strtarget 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
iprcfc 0
tolvrs 0.0

prtcif 1
prtgeo 1



...

[ebousquet]

Dear hameed1987,
You did not send the full error message that gives you what Abinit found wrong in your input file, as mentioned in the error message the problem is printed above.
Best,
Eric

[hameed1987]

Dear Eric

I attached the file of the given error. Please inform me what is wrong with my input file.

Hameed

[ebousquet]

Dear Hameed,
I would like to have your log file where the error messages are printed because the solution will be written there.
Thanks,
Eric

[hameed1987]

Dear Hameed,
I would like to have your log file where the error messages are printed because the solution will be written there.
Thanks,
Eric

Dear Eric,
I could not attached the file of Log, it said the extension is not allowed, so I copied all the file and pasted below.

ABINIT 8.6.3

Give name for formatted input file:
tbase3_1.in
Give name for formatted output file:
tbase3_x.out
Give root name for generic input files:
tbase3_xi
Give root name for generic output files:
tbase3_xo
Give root name for generic temporary files:
tbase3_x

.Version 8.6.3 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu5.4 computer)

.Copyright (C) 1998-2017 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).

ABINIT is a project of the Universite Catholique de Louvain,
Corning Inc. and other collaborators, see ~abinit/doc/developers/contributors.txt .
Please read ~abinit/doc/users/acknowledgments.html for suggested
acknowledgments of the ABINIT effort.
For more information, see https://www.abinit.org .

.Starting date : Mon 5 Aug 2019.
- ( at 11h58 )


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

=== Build Information ===
Version : 8.6.3
Build target : x86_64_linux_gnu5.4
Build date : 20190517

=== Compiler Suite ===
C compiler : gnu5.4
C++ compiler : gnu5.4
Fortran compiler : gnu5.4
CFLAGS : -g -O2 -mtune=native -march=native
CXXFLAGS : -g -O2 -mtune=native -march=native
FCFLAGS : -g -ffree-line-length-none
FC_LDFLAGS :

=== Optimizations ===
Debug level : basic
Optimization level : standard
Architecture : unknown_unknown

=== Multicore ===
Parallel build : yes
Parallel I/O : yes
openMP support : no
GPU support : no

=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : libxc-fallback+atompaw-fallback
FFT flavor : fftw3
LINALG flavor : netlib-fallback
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none

=== Experimental features ===
Bindings : @enable_bindings@
Exports : no
GW double-precision : no

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
-O2 -mtune=native -march=native


Optimizations for 20_datashare:
-O0


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
CPP options activated during the build:

CC_GNU CXX_GNU FC_GNU

HAVE_ATOMPAW HAVE_FC_ALLOCATABLE_DT... HAVE_FC_ASYNC

HAVE_FC_BACKTRACE HAVE_FC_COMMAND_ARGUMENT HAVE_FC_COMMAND_LINE

HAVE_FC_CONTIGUOUS HAVE_FC_CPUTIME HAVE_FC_EXIT

HAVE_FC_FLUSH HAVE_FC_GAMMA HAVE_FC_GETENV

HAVE_FC_IEEE_EXCEPTIONS HAVE_FC_INT_QUAD HAVE_FC_IOMSG

HAVE_FC_ISO_C_BINDING HAVE_FC_ISO_FORTRAN_2008 HAVE_FC_LONG_LINES

HAVE_FC_MOVE_ALLOC HAVE_FC_PRIVATE HAVE_FC_PROTECTED

HAVE_FC_STREAM_IO HAVE_FC_SYSTEM HAVE_FFT

HAVE_FFT_FFTW3 HAVE_FFT_MPI HAVE_FFT_SERIAL

HAVE_FORTRAN2003 HAVE_LIBPAW_ABINIT HAVE_LIBTETRA_ABINIT

HAVE_LIBXC HAVE_MPI HAVE_MPI2

HAVE_MPI_IALLREDUCE HAVE_MPI_IALLTOALL HAVE_MPI_IALLTOALLV

HAVE_MPI_INTEGER16 HAVE_MPI_IO HAVE_MPI_TYPE_CREATE_S...

HAVE_OS_LINUX HAVE_TIMER_ABINIT USE_MACROAVE

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

- input file -> tbase3_1.in
- output file -> tbase3_x.out
- root for input files -> tbase3_xi
- root for output files -> tbase3_xo

-instrng: 81 lines of input have been read from file tbase3_1.in


Please give name of formatted atomic psp file
iofn2 : for atom type 1, psp file is Ge.psp8
read the values zionpsp= 14.0 , pspcod= 8 , lmax= 2

inpspheads: deduce mpsang = 3, n1xccc = 2501.
invars1 : treat image number: 1

symlatt : the Bravais lattice is cP (primitive cubic)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred
symfind : exit, nsym=12
symrel matrices, symafm and tnons are :
1 1 0 0 0 1 0 0 0 1 1 0.0000 0.0000 0.0000
2 -1 0 0 0 -1 0 0 0 -1 1 0.2500 0.2500 0.2500
3 0 1 0 1 0 0 0 0 1 1 0.0000 0.0000 0.0000
4 0 -1 0 -1 0 0 0 0 -1 1 0.2500 0.2500 0.2500
5 0 0 1 1 0 0 0 1 0 1 0.0000 0.0000 0.0000
6 0 0 -1 -1 0 0 0 -1 0 1 0.2500 0.2500 0.2500
7 1 0 0 0 0 1 0 1 0 1 0.0000 0.0000 0.0000
8 -1 0 0 0 0 -1 0 -1 0 1 0.2500 0.2500 0.2500
9 0 1 0 0 0 1 1 0 0 1 0.0000 0.0000 0.0000
10 0 -1 0 0 0 -1 -1 0 0 1 0.2500 0.2500 0.2500
11 0 0 1 0 1 0 1 0 0 1 0.0000 0.0000 0.0000
12 0 0 -1 0 -1 0 -1 0 0 1 0.2500 0.2500 0.2500

symlatt : the Bravais lattice is cP (primitive cubic)

symlatt : the Bravais lattice is cP (primitive cubic)

--- !COMMENT
src_file: symbrav.F90
src_line: 201
message: |
The Bravais lattice determined only from the primitive
vectors, bravais(1)= 7, is more symmetric
than the real one, iholohedry= 5, obtained by taking into
account the atomic positions. Start deforming the primitive vector set.
...


symlatt : the Bravais lattice is hR (rhombohedral)
symspgr : spgroup= 166 R-3 m (=D3d^5)
symspgr : optical characteristics = uniaxial
Optical axis (in reduced coordinates, real space ) : 1 1 1
ingeo : angdeg(1:3)= 90.00000000 90.00000000 90.00000000
invars2: take the default value of fband= 1.25000000E-01
chkneu : initialized the occupation numbers for occopt= 1, spin-unpolarized or antiferromagnetic case :
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 0.00 0.00
npfft, npband, npspinor and npkpt: 1 1 1 4

--- !WARNING
src_file: distrb2.F90
src_line: 113
message: |
nkpt*nsppol (91) is not a multiple of nproc_kpt (4)
The k-point parallelisation is not efficient.
...

mpi_setup: mkmem undefined in the input file.Use default mkmem = nkpt
mpi_setup: With nkpt_me=23 and mkmem = 91, ground state wf handled in core.
Resetting mkmem to nkpt_me to save memory space.
mpi_setup: mkqmem undefined in the input file.Use default mkqmem = nkpt
mpi_setup: With nkpt_me=23 and mkqmem = 91, ground state wf handled in core.
Resetting mkqmem to nkpt_me to save memory space.
mpi_setup: mk1mem undefined in the input file.Use default mk1mem = nkpt
mpi_setup: With nkpt_me=23 and mk1mem = 91, ground state wf handled in core.
Resetting mk1mem to nkpt_me to save memory space.
For input ecut= 3.100000E+01 best grid ngfft= 54 54 54
max ecut= 3.146833E+01

==== FFT mesh ====
FFT mesh divisions ........................ 54 54 54
Augmented FFT divisions ................... 55 55 54
FFT algorithm ............................. 312
FFT cache size ............................ 16
getmpw: optimal value of mpw= 10108

Symmetries : space group R-3 m (#166); Bravais hR (rhombohedral)

getdim_nloc : deduce lmnmax = 18, lnmax = 6,
lmnmaxso= 18, lnmaxso= 6.
memory : analysis of memory needs
================================================================================
Values of the parameters that define the memory need of the present run
intxc = 0 ionmov = 3 iscf = 7 lmnmax = 6
lnmax = 6 mgfft = 54 mpssoang = 3 mqgrid = 3001
natom = 2 nloc_mem = 1 nspden = 1 nspinor = 2
nsppol = 1 nsym = 12 n1xccc = 2501 ntypat = 1
occopt = 1 xclevel = 2
- mband = 30 mffmem = 1 mkmem = 23
mpw = 10108 nfft = 157464 nkpt = 91
================================================================================
P This job should need less than 266.844 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
_ WF disk file : 421.066 Mbytes ; DEN or POT disk file : 1.203 Mbytes.
================================================================================

Biggest array : cg(disk), with 106.4247 MBytes.
memana : allocated an array of 106.425 Mbytes, for testing purposes.
memana: allocated 266.844Mbytes, for testing purposes.
The job will continue.
--------------------------------------------------------------------------------
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- iomode0 = 0 , fftalg0 =312 , wfoptalg0 = 0
-
- outvars: echo of global parameters not present in the input file
- max_nthreads = 0
-
-outvars: echo values of preprocessed input variables --------
acell 1.0692070460E+01 1.0692070460E+01 1.0692070460E+01 Bohr
amu 7.26100000E+01
chksymbreak 0
chksymbreak 0
diemac 1.20000000E+01
ecut 3.10000000E+01 Hartree
ecutsm 5.00000000E-01 Hartree
- fftalg 312
ionmov 3
ixc 11
kpt -8.33333333E-02 -1.66666667E-01 0.00000000E+00
-8.33333333E-02 -8.33333333E-02 8.33333333E-02
-8.33333333E-02 -3.33333333E-01 0.00000000E+00
-1.66666667E-01 -2.50000000E-01 0.00000000E+00
-8.33333333E-02 -2.50000000E-01 8.33333333E-02
-1.66666667E-01 -1.66666667E-01 8.33333333E-02
-8.33333333E-02 -1.66666667E-01 1.66666667E-01
-8.33333333E-02 -8.33333333E-02 2.50000000E-01
-8.33333333E-02 5.00000000E-01 0.00000000E+00
-1.66666667E-01 -4.16666667E-01 0.00000000E+00
-8.33333333E-02 -4.16666667E-01 8.33333333E-02
-2.50000000E-01 -3.33333333E-01 0.00000000E+00
-1.66666667E-01 -3.33333333E-01 8.33333333E-02
-8.33333333E-02 -3.33333333E-01 1.66666667E-01
-2.50000000E-01 -2.50000000E-01 8.33333333E-02
-1.66666667E-01 -2.50000000E-01 1.66666667E-01
-8.33333333E-02 -2.50000000E-01 2.50000000E-01
-1.66666667E-01 -1.66666667E-01 2.50000000E-01
-8.33333333E-02 -1.66666667E-01 3.33333333E-01
-8.33333333E-02 -8.33333333E-02 4.16666667E-01
-8.33333333E-02 3.33333333E-01 0.00000000E+00
-1.66666667E-01 4.16666667E-01 0.00000000E+00
-2.50000000E-01 5.00000000E-01 0.00000000E+00
-1.66666667E-01 5.00000000E-01 8.33333333E-02
-3.33333333E-01 -4.16666667E-01 0.00000000E+00
-2.50000000E-01 -4.16666667E-01 8.33333333E-02
-1.66666667E-01 -4.16666667E-01 1.66666667E-01
-8.33333333E-02 -4.16666667E-01 2.50000000E-01
-3.33333333E-01 -3.33333333E-01 8.33333333E-02
-2.50000000E-01 -3.33333333E-01 1.66666667E-01
-1.66666667E-01 -3.33333333E-01 2.50000000E-01
-8.33333333E-02 -3.33333333E-01 3.33333333E-01
-2.50000000E-01 -2.50000000E-01 2.50000000E-01
-1.66666667E-01 -2.50000000E-01 3.33333333E-01
-8.33333333E-02 -2.50000000E-01 4.16666667E-01
-1.66666667E-01 -1.66666667E-01 4.16666667E-01
-8.33333333E-02 -1.66666667E-01 5.00000000E-01
-8.33333333E-02 -8.33333333E-02 -4.16666667E-01
-8.33333333E-02 1.66666667E-01 0.00000000E+00
-1.66666667E-01 2.50000000E-01 0.00000000E+00
-2.50000000E-01 3.33333333E-01 0.00000000E+00
-3.33333333E-01 4.16666667E-01 0.00000000E+00
-4.16666667E-01 5.00000000E-01 0.00000000E+00
-3.33333333E-01 5.00000000E-01 8.33333333E-02
-2.50000000E-01 5.00000000E-01 1.66666667E-01
-4.16666667E-01 -4.16666667E-01 8.33333333E-02
-3.33333333E-01 -4.16666667E-01 1.66666667E-01
-2.50000000E-01 -4.16666667E-01 2.50000000E-01
-1.66666667E-01 -4.16666667E-01 3.33333333E-01
-8.33333333E-02 -4.16666667E-01 4.16666667E-01
outvar_i_n : Printing only first 50 k-points.
kptrlatt 6 -6 6 -6 6 6 -6 -6 6
kptrlen 1.11115256E+02
P mkmem 23
natom 2
nband 30
ngfft 54 54 54
nkpt 91
nspinor 2
nsym 12
ntime 100
ntypat 1
occ 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
1.000000 1.000000 1.000000 1.000000 0.000000 0.000000
optcell 2
optforces 1
pawecutdg 6.20000000E+01 Hartree
pawovlp -1.0000000000E+00
prtcif 1
prtgeo 1
shiftk 5.00000000E-01 5.00000000E-01 5.00000000E-01
spgroup 166
symrel 1 0 0 0 1 0 0 0 1 -1 0 0 0 -1 0 0 0 -1
0 1 0 1 0 0 0 0 1 0 -1 0 -1 0 0 0 0 -1
0 0 1 1 0 0 0 1 0 0 0 -1 -1 0 0 0 -1 0
1 0 0 0 0 1 0 1 0 -1 0 0 0 0 -1 0 -1 0
0 1 0 0 0 1 1 0 0 0 -1 0 0 0 -1 -1 0 0
0 0 1 0 1 0 1 0 0 0 0 -1 0 -1 0 -1 0 0
tnons 0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
0.0000000 0.0000000 0.0000000 0.2500000 0.2500000 0.2500000
toldfe 1.00000000E-22 Hartree
tolmxf 5.00000000E-08
typat 1 1
wtk 0.01389 0.00694 0.01389 0.01389 0.01389 0.00694
0.01389 0.00694 0.01389 0.01389 0.01389 0.01389
0.01389 0.01389 0.00694 0.01389 0.01389 0.00694
0.01389 0.00694 0.01389 0.01389 0.01389 0.01389
0.01389 0.01389 0.01389 0.01389 0.00694 0.01389
0.01389 0.01389 0.00694 0.01389 0.01389 0.00694
0.01389 0.00694 0.01389 0.01389 0.01389 0.01389
0.01389 0.01389 0.01389 0.00694 0.01389 0.01389
0.01389 0.01389
outvars : Printing only first 50 k-points.
xangst 1.4145000000E+00 1.4145000000E+00 1.4145000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
xcart 2.6730176150E+00 2.6730176150E+00 2.6730176150E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
xred 2.5000000000E-01 2.5000000000E-01 2.5000000000E-01
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
znucl 32.00000

================================================================================

chkinp: Checking input parameters for consistency.

--- !ERROR
src_file: chkinp.F90
src_line: 2629
mpi_rank: 0
message: |
so_psp( 1) was input as 1, with nspinor=2 and usepaw=0.
This requires a treatment of the spin-orbit interaction. However, it has been detected
that the pseudopotential that you want to use does not specify the spin-orbit coupling.
Action: choose a pseudopotential that contains information about the spin-orbit interaction,
or deliberately switch off the spin-orbit interaction by setting so_psp=0 for that pseudopotential in the input file.
...


--- !ERROR
src_file: chkinp.F90
src_line: 3388
mpi_rank: 0
message: |
Checking consistency of input data against itself gave 1 inconsistency.
The details of the problem can be found above.
...


leave_new: decision taken to exit ...
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 14.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[hameed-ubuntu:05163] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[hameed-ubuntu:05163] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages


--- !ERROR
src_file: chkinp.F90
src_line: 3388
mpi_rank: 3
message: |
Checking consistency of input data against itself gave 1 inconsistency.
The details of the problem can be found above.
...



Hameed

[ebousquet]

Dear Hameed,
I think the error message is clear:

--- !ERROR
src_file: chkinp.F90
src_line: 2629
mpi_rank: 0
message: |
so_psp( 1) was input as 1, with nspinor=2 and usepaw=0.
This requires a treatment of the spin-orbit interaction. However, it has been detected
that the pseudopotential that you want to use does not specify the spin-orbit coupling.
Action: choose a pseudopotential that contains information about the spin-orbit interaction,
or deliberately switch off the spin-orbit interaction by setting so_psp=0 for that pseudopotential in the input file.
...

Eric