ABINIT Discussion Forums

Dear all,

I'm performing a bfgs relaxation of a As A7 cell and during it, in the log file, I encounter a warning

WARNING: ATOMIC COORDINATES WERE SYMMETRIZED
DIFFERENCES:
-3.24740234702858288E-015 -3.30291349825984071E-015 -3.21964677141295397E-015
-2.99760216648792266E-015 -2.99760216648792266E-015 -3.21964677141295397E-015

I don't remember seeing this warning in the previous versions of the code (bellow version 6). I'm not sure if I understand the true meaning of this warning. Does it mean that during the relaxation the code itself has symmetrised the coordinates of the atoms due to the symmetries of the unit cell? If it is, I don't understand why does it do that, since the z components of the atomic coordinated should be one of the degrees of freedom. The input file is bellow.

I notice also that abinit changes xreds from

xred 0.00 0.00 0.23
0.00 0.00 0.77

to

xred 2.3000000000E-01 2.3000000000E-01 2.3000000000E-01
7.7000000000E-01 7.7000000000E-01 7.7000000000E-01

in the input echo. The relaxation, with the warning mentioned above, gives

xred12 2.5000021927E-01 2.5000021927E-01 2.5000021927E-01
7.4999978073E-01 7.4999978073E-01 7.4999978073E-01

SCF converges nicely, but I managed to get the forces under the wanted tolerance only when I commented out the fixing of the atomic coordinates.

Also, the code changes the hexagonal cell defined with

acell 2*7.591 21.745
angdeg 90 90 120
spgroup 166
brvltt -1

into

acell12 6.6535843474E+00 6.6535843474E+00 6.6535843474E+00 Bohr
rprim12 5.3776310315E-01 3.1047767237E-01 7.8384594140E-01
-5.3776310315E-01 3.1047767237E-01 7.8384594140E-01
0.0000000000E+00 -6.2095534473E-01 7.8384594140E-01



Any comments and answers of how to overcome this problem would be appreciated.

Yours,

igor Lukacevic


Input file

#As A7
#Structural optimization run

ndtset 2
udtset 1 2

# Set 1 : Internal coordinate optimization

ionmov?1 2
ntime?1 50
optcell?1 0
tolmxf?1 5.0e-7
#natfixx?1 2
#iatfixx?1 1 2
#natfixy?1 2
#iatfixy?1 1 2

# Set 2 : Lattice parameter relaxation (including re-optimization of
# internal coordinates)

dilatmx?2 1.15
getxred?2 -1
getwfk?2 -1
ionmov?2 2
ntime?2 50
optcell?2 2
tolmxf?2 5.0e-7
strfact?2 50
strprecon?2 0.1
#natfixx?2 2
#iatfixx?2 1 2
#natfixy?2 2
#iatfixy?2 1 2

#Common input data

#strtarget -0.00142755018 -0.00142755018 -0.00142755018 0.0 0.0 0.0 #targeting 42 GPa

#Starting approximation for the unit cell
acell 2*7.591 21.745
angdeg 90 90 120
spgroup 166
brvltt -1

#Definition of the atom types and atoms
natom 2
ntypat 1
typat 2*1
znucl 33

#Starting approximation for atomic positions in REDUCED coordinates
xred 0.00 0.00 0.23
0.00 0.00 0.77

#Gives the number of bands, explicitely (do not take the default)
nband 10
occopt 3
tsmear 0.001

#Definition of the plane wave basis set
ecut 10
ecutsm 0.5

#Definition of the k-point grid
kptopt 1
ngkpt 6 6 2
chksymbreak 0

#Definition of the self-consistency procedure
iscf 7 # Use Pulay mixing sheme for SCF cycle
#npulayit 7 # Number of Pulay iterations
# nnsclo 2 # Number of non-self consistent loops
# nline 6 # Number of line minimisations
nstep 100 # Maxiumum number of SCF iterations
# tolvrs 1.0d-18
toldff 1.0e-8

#Define xc approximation
ixc 1

timopt 2