ABINIT Discussion Forums

Dear Abinit user
iam confusing with my input file which always had failed. can some want correct it for me ?
This my input file:
#struktur silicene
#test DOS menggunakan metode tetrahedron

ndtset 2
#dataset 1 : SCF calculation
ngkpt1 2 2 2
toldfe1 1.0d-10
prtden1 1

#dataset 2 : DOS calculation
iscf2 -3
getden2 1
getwfk2 1
prtdos2 3
dosdeltae 0.00005
ngkpt2 12 12 1
tolwfr2 1.0d-16
shiftk2 0 0 0
natsph2 2
iatsph2 1 2
ratsph2 2 2.75


acell 8.2 8.2 15.0 Angstrom
rprim
0.866 0.5 0
0.0 1.0 0.0
0.0 0.0 1.0
nspinor 2
#Definition of the atom types
ntypat 3 # There is only one type of atom
znucl 32 33 01 # 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 17 # There are two atoms
typat 2 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3
xred
1.5/6 3/6 0.15
1/6 1/6 0
2/6 2/6 0
4/6 1/6 0
5/6 2/6 0
1/6 4/6 0
2/6 5/6 0
4/6 4/6 0
5/6 5/6 0
1/6 1/6 0.5/6
2/6 2/6 0.5/6
4/6 1/6 0.5/6
5/6 2/6 0.5/6
1/6 4/6 0.5/6
2/6 5/6 0.5/6
4/6 4/6 0.5/6
5/6 5/6 0.5/6
ecut 30.0
nstep 20
diemac 12.0
optforces 1
chkprim 0
kptopt 1
nshiftk 1
shiftk 0.0 0.0 0.0
ngkpt 12 12 1
nband 40
occopt 3
tsmear 0.006


This is log file:
ABINIT

Give name for formatted input file:
t46.in
Give name for formatted output file:
t46.out
Give root name for generic input files:
tbase3_x
Give root name for generic output files:
tbase3_4xi
Give root name for generic temporary files:
tbase3_3xo

--- !WARNING
message: |
Finds that output file t46.out
already exists.
src_file: Subroutine Unknown
src_line: 0
...

new name assigned:t46.out


--- !WARNING
message: |
Finds that output file t46.out
already exists.
src_file: Subroutine Unknown
src_line: 0
...

new name assigned:t46.outA


--- !WARNING
message: |
Finds that output file t46.outA
already exists.
src_file: Subroutine Unknown
src_line: 0
...

new name assigned:t46.outB


--- !WARNING
message: |
Finds that output file t46.outB
already exists.
src_file: Subroutine Unknown
src_line: 0
...

new name assigned:t46.outC


--- !WARNING
message: |
Finds that output file t46.outC
already exists.
src_file: Subroutine Unknown
src_line: 0
...

new name assigned:t46.outD


--- !WARNING
message: |
The starting date is more than 3 years after the initial release
of this version of ABINIT, namely Jul 2014.
This version of ABINIT is not supported anymore.
Action : please, switch to a more recent version of ABINIT.
src_file: Subroutine Unknown
src_line: 0
...


.Version 7.8.2 of ABINIT
.(sequential version, prepared for a x86_64_linux_gnu5.2 computer)

.Copyright (C) 1998-2014 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 http://www.abinit.org .

.Starting date : Thu 19 Oct 2017.
- ( at 13h40 )


--- !WARNING
message: |
The starting date is more than 3 years after the initial release
of this version of ABINIT, namely Jul 2014.
This version of ABINIT is not supported anymore.
Action : please, switch to a more recent version of ABINIT.
src_file: Subroutine Unknown
src_line: 0
...


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

=== Build Information ===
Version : 7.8.2
Build target : x86_64_linux_gnu5.2
Build date : 20151122

=== Compiler Suite ===
C compiler : gnu5.2
C++ compiler : gnu5.2
Fortran compiler : gnu5.2
CFLAGS : -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
CXXFLAGS : -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
FCFLAGS : -g -O2 -fstack-protector-strong
FC_LDFLAGS :

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

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

=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : none
FFT flavor : none
LINALG flavor : netlib
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none

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

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


++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Default optimizations:
--- None ---


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


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

CC_GNU CXX_GNU FC_GNU

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_PRIVATE HAVE_FC_PROTECTED HAVE_FC_STREAM_IO

HAVE_FC_SYSTEM HAVE_FORTRAN2003 HAVE_LIBPAW_ABINIT

HAVE_LINALG HAVE_LINALG_SERIAL HAVE_OS_LINUX

HAVE_TIMER HAVE_TIMER_ABINIT HAVE_TIMER_SERIAL

USE_MACROAVE
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

- input file -> t46.in
- output file -> t46.outD
- root for input files -> tbase3_x
- root for output files -> tbase3_4xi

-instrng : 89 lines of input have been read from file t46.in


iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 1 , psp file is 32-Ge.GGA.fhi

iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 2 , psp file is 33-As.GGA.fhi

iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 3 , psp file is 01-H.GGA.fhi
read the values zionpsp= 4.0 , pspcod= 6 , lmax= 3
read the values zionpsp= 5.0 , pspcod= 6 , lmax= 3
read the values zionpsp= 1.0 , pspcod= 6 , lmax= 3

inpspheads: deduce mpsang = 4, n1xccc = 0.

invars1m : enter jdtset=1
invars1 : treat image number 1

symlatt : the Bravais lattice is oC (one-face-centered orthorhombic)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is oC (one-face-centered orthorhombic)

symlatt : the Bravais lattice is oC (one-face-centered orthorhombic)

--- !COMMENT
message: |
The Bravais lattice determined only from the primitive
vectors, bravais(1)= 3, is more symmetric
than the real one, iholohedry= 2, obtained by taking into
account the atomic positions. Start deforming the primitive vector set.
src_file: Subroutine Unknown
src_line: 0
...


symlatt : the Bravais lattice is mP (primitive monoclinic)
symspgr : spgroup= 3 P2 (=C2^1)
Simple Lattice Grid

invars1m : enter jdtset=2

inread : ERROR -
Attempted to read ndig=5 floating point digits,
from string(1:ndig) ACELL, to initialize a floating variable.

inarray :
An error occurred reading data for keyword " RATSPH2",
looking for 3 array elements.
DATA TYPE INFORMATION:
REAL: Data type name: REAL(DP)
Kind value: 8
Precision: 15
Smallest nonnegligible quantity relative to 1: 0.22204460E-15
Smallest positive number: 0.22250739-307
Largest representable number: 0.17976931+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
MPI-IO support is OFF

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

=== Build Information ===
Version : 7.8.2
Build target : x86_64_linux_gnu5.2
Build date : 20151122

=== Compiler Suite ===
C compiler : gnu5.2
C++ compiler : gnu5.2
Fortran compiler : gnu5.2
CFLAGS : -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
CXXFLAGS : -g -O2 -fstack-protector-strong -Wformat -Werror=format-security
FCFLAGS : -g -O2 -fstack-protector-strong
FC_LDFLAGS :

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

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

=== Connectors / Fallbacks ===
Connectors on : yes
Fallbacks on : yes
DFT flavor : none
#0 0x7FC27C40AE08
#1 0x1139F2E
#2 0xEADC7F
#3 0xEAB04A
#4 0xC6FC3B
#5 0xC4A339
#6 0xC0125E
#7 0x4040BE
#8 0x403CFC
#9 0x7FC27BB2682F
#10 0x403D38
#11 0xFFFFFFFFFFFFFFFF
FFT flavor : none
LINALG flavor : netlib
MATH flavor : none
TIMER flavor : abinit
TRIO flavor : none

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

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


--- !ERROR
message: |
There is a problem with the input file : maybe
a disagreement between the declared dimension of the array,
and the number of data actually provided.
Action: correct your input file !
src_file: Subroutine Unknown
src_line: 0
...


leave_new : decision taken to exit ...

--- !ERROR
message: |
There is a problem with the input file : maybe
a disagreement between the declared dimension of the array,
and the number of data actually provided.
Action: correct your input file !
src_file: Subroutine Unknown
src_line: 0
...

Hello TriSugiono,

Thank you for posting both your input file and the Abinit log file. The log file is often useful in telling you what is wrong (i.e. it gives error messages at the end of the file) and often can point you to a solution. In this case, the error messages indicate a problem in the input file and, above the build information, you will find a sections of lines which say



Which tells you that the program is attempting to read the variable ACELL and look for numbers with at least 5 floating point digits. In this case, you have provided numbers with only a single decimal place and therefore an error message is printed out and the program ends.

In general, Abinit needs more digits for the numbers that you, as the user, provide (I personally provide at least 9 after the decimal place). This is true for variables such as acell, xred, xcart, rprim etc. Here your use of fractions for xred is good as Abinit can handle simple fractions.

Please let us know if you have more questions!

Hello Npike
Thanks for your reply
That solve my problem, actually i don't get what parameter must be changed. but for now that's things solve my problem. But usually the abinit recognizes fractions that are automatically changed in decimal form. But for now that's things solve my problem.

Hello again,

I am glad to read that things are working for you now.

To clarify:

Your original code was

acell 8.2 8.2 15.0 Angstrom

And Abinit had a problem with the number of decimal places you used.

The corrected input file should have

acell 8.200000 8.200000 15.00000 Angstrom


Does that help clear things up?

Hello again,

i am not change the acell number, but now working. i think if we input acell number except bohr number , abinit will automatically exchange it to bohr.
it work for now and my task complete and i can get another research.
Thanks for your help.