ABINIT Discussion Forums

maybe you should try PAW psps http://www.abinit.org/downloads/PAW2 - it can speed up the calculation (note that you can not upload these PAW pseudos to nanohub), but I think it is not too necessarily now.

Best wishes, Maxim

Dear Maxim,
long time, look at this statements from my log file,

" symlatt : the Bravais lattice is cP (primitive cubic)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is cP (primitive cubic)

symlatt : the Bravais lattice is cP (primitive cubic)

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

symlatt : the Bravais lattice is hR (rhombohedral)

symbrav : COMMENT -
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 5, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.
symlatt : the Bravais lattice is mC (one-face-centered monoclinic)

symbrav : COMMENT -
The Bravais lattice determined from modified primitive
vectors, bravais(1)= 2, has a lower symmetry than before,
but is still more symmetric than the real one, iholohedry= 1
obtained by taking into account the atomic positions.

symlatt : the Bravais lattice is aP (primitive triclinic)
symspgr : the symmetry operation no. 1 is the identity
symspgr : spgroup= 1 P1 (=C1^1)
inkpts : enter
getkgrid : length of smallest supercell vector (bohr)= 1.480000E+01
Simple Lattice Grid"

Now thus this mean that my doped system is primitive triclinic.
Thanks

So the calculation is succeed?

my best wishes Maxim

Dear Maxim

I want to create 1x1x3 supercell of Bi2S3. İts space group R-3m (#166).But
I dont know how I creat 1x1x3 süpercell (along z-axes).my input file is as a following. Can you help me to do 1x1x3 supercell.

Best regards...

# Bi2Se3 : computation of the total energy
# Convergence with respect to the number of k points.

ndtset 6

#Definition of the k-point grids
kptopt 1 # Option for the automatic generation of k points, taking
# into account the symmetry
#nshiftk 4
#shiftk 0.5 0.5 0.5 # These shifts will be the same for all grids
#0.5 0.0 0.0
#0.0 0.5 0.0
#0.0 0.0 0.5

#ngkpt1 2 2 2 # Definition of the different grids
#ngkpt2 4 4 4
#ngkpt3 6 6 6
ngkpt4 8 8 8
ecut: 18 ecut+ 2

getwfk -1 # This is to speed up the calculation, by restarting
# from previous wavefunctions, transferred from the old
# to the new k-points.



#Definition of the unit cell
acell 3*18.6 # This is equivalent to 10.18 10.18 10.18

angdeg 3*24


#Definition of the atom types
ntypat 2 # There is only one type of atom
znucl 83 34 # 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 5 # There are two atoms
typat 2*1 3*2 # They both are of type 1, that is, Silicon
xred # This keyword indicate that the location of the atoms
# will follow, one triplet of number for each atom
0.399 0.399 0.399
-0.399 -0.399 -0.399
0.0 0.0 0.0
0.206 0.206 0.206
-0.206 -0.206 -0.206


#Definition of the planewave basis set
#ecut 8.0 # Maximal kinetic energy cut-off, in Hartree

#Definition of the SCF procedure
nstep 1000 # Maximal number of SCF cycles
toldfe 1.0d-6 # Will stop when, twice in a row, the difference
# between two consecutive evaluations of total energy
# differ by less than toldfe (in Hartree)
#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
# is described in the "dielng" input variable section.
# Here, we follow the prescription for bulk silicon.

You should simply do:
if x y z is initial state, then:
x y z/3
x y (z/3)+(1/3)
x y (z/3)+(2/3)
is your 1x1x3 supercell.

Best wishes, Maxim

Dear Maxim,
thanks your reply.

then how should I define acell or rprim of crystals. If I define acell as a=18.6 b=18.6 c=3x18.6=55.8, is it correct.

Dear sevket simsek,

I think that it is correct. You may check this supercell simly by plotting it in e. g. Diamond.

Best wishes, Maxim.

Does your dopant has the same valence as the host cation, or different? If the same, then maybe you can not create a supercell, and use mixalch only. If different valence, then it is necessary to create vacancies in a supercell and use mixalch simultaneously. You can check valencies here http://materialsproject.org/janrain/log ... predictor/ (Sign Up and select your elements) and https://materialsproject.org/wiki/index ... l_an_2.png.

Maybe to set initial value of acell maximally close to your case (doping and solid solution) you should consider Vegard rule http://www.google.ru/search?q=vegard+ru ... e&ie=UTF-8.

Best wishes, Maxim.

Dear Maxim,
I have little problem on how to run abinit on nanohub, also my hub is looking for java software. Kindly help me out of this two problems. Thanks

If you have windows then maybe 2install java proceed e. g. https://nanohub.org/kb/misc/java;
nanohub requires rprim - so you should put
in case if you have ortogonal system, in other cases run at your local PC for e.g. 10 minutes (it's enough time for symmetry finder of abinit), then terminate job and look in rprim in *.out or *.log.
Nonohub has very limited disc space, so use this:

My file is attached here. It does work.
You have acess to this forum - so you surely will have acess to nanohub - you need PC and internet for a little time to submit job and to take results after some time.

Merry christmas and happy new year!

Dear Maxim,
Thanks alot. Happy new year

Dear Maxim,
is it every material that i dope will be primitive triclinic ?. look at the following from my log file.
CaB6 is doped with Ba, and i have this
DATASET 11 : space group P1 (# 1); Bravais aP (primitive triclinic)
================================================================================
Values of the parameters that define the memory need for DATASET 11.
intxc = 0 ionmov = 2 iscf = 7 xclevel = 2
lmnmax = 8 lnmax = 8 mband = 9 mffmem = 1
P mgfft = 80 mkmem = 4 mpssoang= 4 mpw = 30451
mqgrid = 3874 natom = 7 nfft = 512000 nkpt = 4
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 1 n1xccc = 2501 ntypat = 2 occopt = 1
================================================================================


And for MgB2 doped with Ca, i have this
DATASET 1 : space group P1 (# 1); Bravais aP (primitive triclinic)
================================================================================
Values of the parameters that define the memory need for DATASET 1.
intxc = 0 ionmov = 2 iscf = 7 xclevel = 2
lmnmax = 8 lnmax = 8 mband = 5 mffmem = 1
P mgfft = 64 mkmem = 365 mpssoang= 4 mpw = 10938
mqgrid = 3010 natom = 3 nfft = 186624 nkpt = 365
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 1 n1xccc = 2501 ntypat = 2 occopt = 1
================================================================================

I think this means that doped system in both cases are primitive triclinic.

The second question is that if i get value of lattice parameter a, how am i going to get b and c parameters
Prof thanks alot for your usual understanding.

-Bamgbose.

Because you use nsym=1 (this blocks symmetry finder of abinit), abinit will always recognize your structure as primitive triclinic, even if it has symmetry. Maybe you can take your final optimized coordinates and re-run with nsym=0 (with symmetry finder enabled) to see which symmetry your optimized cell have. You can terminate your job after a small time - symmetry finder launches before any SCF iterations (use input file without relaxation and with nstep 1-2 only). Perhaps there are other ways to recognize symmetry of your optimized cell.


Best wishes, Maxim.

Dear Maxim,
Thanks alot for your usual assistance all along. The real thing i want to find out now is that if i dope a cubic structure will the doped system remain cubic ? Please explain what actually happens whenever i dope as per their structures.
Thanks.

Dear Maxim,
kind held me to do necessary correction to this file so that the output etot vs acell will give me a parabola.
# Crystalline ScAlN : computation of the total energy

# definition of unit cell
diemac 12
ndtset 10
acell: 3*8.3
acell+ 3*0.1
chksymbreak 0
chkprim 0
rprim 0 0.5 0.5
0.5 0 0.5
0.5 0.5 0

#alchemical input
znucl 7 21 13
nband 36
ntypat 3
natom 2
npsp 3
typat 1 2
#ntypalch 1
mixalch 0.95 0.05



xred 0.0 0.0 0.0
0.5 0.5 0.5


#Relaxation inputs
optcell 1
ionmov 3
ntime 20
dilatmx 1.1
ecutsm 0.5
strfact 100
tolmxf 5.0d-5

#SCF procedure
nstep 20
toldfe 1.0d-7
iscf 7

#Examine multiple cutoff energies
getwfk -1
ecut 40

#Definition of the k-point grids
kptopt 1
nshiftk 4
shiftk 0.5 0.5 0.5
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0

ngkpt 4 4 4
occopt 1

Thanks for your usual assistance.