ABINIT Discussion Forums

Dear List,

I am a newbie in abinit, and trying to study the interaction of gas molecules on graphene systems.
In my case, the default examples in tests/* are working correctly with sequential version of ABINIT, But I got an error message
when I use a SCF calculation input of Graphene (of 1x1 unitcell of graphene, C-C bondlenght=1.42 angst):

My Input
=============================================
# Definition of the unit cell unit: Bohr
acell 1 1 1
rprim 2.323902 2.061751 0.00000
2.323902 -2.061751 0.00000
0.000000 0.000000 6.00000

# Definition of the atom types
ntypat 1
znucl 6

# functional GGA PBE
ixc 11

# Definition of the atoms
natom 2
typat 1 1

# XYZ geometry of the system unit: Amstrong
xangst
1.420000 0.00000 0.00000
2.840000 0.00000 0.00000

# Definition of the planewave basis set
ecut 8

#Definition of the k-point grid
ngkpt 2 2 1

# no optimization
ionmov 0
optcell 0

# Definition of the SCF procedure
iscf 7
npulayit 7
nstep 111
toldfe 1.0e-4
diemac 2

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


Error message:-
-------------------------------------------------------------------------------------
- root for output files -> ge.raw_OUTPUT

instrng : 38 lines of input have been read

iofn2 : Please give name of formatted atomic psp file
iofn2 : for atom type 1 , psp file is /opt/abinit.raw/abinit-6.4.2/tests/Psps_for_tests/6c_lda.paw
read the values zionpsp= 4.0 , pspcod= 7 , lmax= 1
2 : shape_type[,lambda,sigma]


inpspheads : deduce mpsang = 2, n1xccc = 1.

invars1m : enter jdtset= 0
invars1 : treat image number 1
forrtl: severe (61): format/variable-type mismatch, unit -5, file Internal Formatted Write
Image PC Routine Line Source
libirc.so F7CAC1BC Unknown Unknown Unknown
libirc.so F7CA142F Unknown Unknown Unknown
libifcore.so.5 F7FAB860 Unknown Unknown Unknown
libifcore.so.5 F7F3579B Unknown Unknown Unknown
libifcore.so.5 F7F3546E Unknown Unknown Unknown
libifcore.so.5 F7F68EB7 Unknown Unknown Unknown
abinit 091BD8FA Unknown Unknown Unknown
--------------------------------------------------------------------------------------

Till now I have no idea about this error log! Please note that I use the PSP: tests/Psps_for_tests/6c_lda.paw, and tried many
combinationas of keywords in the section of SCF. But it didnt help me.

Does anyone has an idea on this error?

I hope somebody can easily give an idea on the cause of error...

Thanks in advance

Mohan

Dear Mohan,

6c_lda.paw is a projector augmented wave pseudopotential file but there is no PAW variable in your input. Look at http://www.abinit.org/documentation/helpfiles/for-v6.4/input_variables/varpaw.html

Alain

Dear Mohan

ixc=11 is for GGA but you used lda and paw psudopotential !!
paw needs its own variables in input file.
but you can use GGA psudopotentials and be carefull that the value of
ixc in your input file must be equal to pspxc in Pseudopotential(Psp file)
so check it first!
you can find the Psp with pspxc=11 in abinit.org---->Atomic data file------>norm-conserving Pseudopotentials
------->Fritz-Haber-Institute (FHI) pseudopotentials.

fariba

Typically it's not necessary to specify ixc in the input file at all. Provided you are using either norm conserving pseudopotentials all made with the same exchange/correlation functional, or PAW data sets all made with the same exchange/correlation functional, abinit will read ixc from these files and use it. And, of course, it is definitely not recommended to mix different exchange/correlation functionals within the same calculation (unless you are doing so for a very specific reason).

dear Alain, Fariba, and Prof. J W Zwanziger,
Thank you verymuch for your comments; My input file is now working; It avoid PAW information and XC keyword is now take from PSP file as by Zwanzigers suggestion. In this case I used 06-C.GGA.fhi (pspxc=11). I also found nanoHubs Input make tool is helpful and can be used to trace out mistakes by even trying a real cluster simulation! (Thanks to Purdue Uty.). I also made a correct change in rprim , since it takes value in Bohr.

My working input is

============================O
# Definition of the unit cell
acell 1 1 1
rprim 4.025116356 -1.808156919 0.00000000
4.025116356 1.808156919 0.00000000
0.000000000 0.000000000 6.00000000

# Definition of the atom types
ntypat 1
znucl 6

# Definition of the atoms
natom 2
typat 1 1
xangst
1.42 0.00 0.00
2.84 0.00 0.00

# Definition of the Planewave basis set
ecut 12

# SCF definition
iscf 2
nstep 25
diemac 12.0
nsppol=1
toldfe 1.0e-08
============================O

hai

I would like to study the effects of defects on the electronic properties of graphene. I am trying to write the abinit code for the simplest defect in graphene, a single missing atom in the supercell of graphene.
Can anyone help me to write the code for a single vacancy in a 4*4*4 supercell of graphene?
I tried to simulate the band structure of the unit cell of graphene containing two carbon atoms.
I don't know how to write the code for simulating a 4*4*4 supercell of graphene. If I use the abinit input variable "acell " as follows:

acell 4 4 4 whether this acell implies the size of the supercell?

Thanks and Regards
Seba