The ABINIT Users Mailing List ( CLOSED )

[mkosmows@syr.edu]

Dear Abinit Community:

I am getting a "This is further away from every atom in crystal than the 
allowed tolerance." error in my log file after a calculation. Further 
examination of this error text shows that the deviation distance from the 
expected position is the same as the precision of my original coordinates 
(x-ray structure with H position to only 0.001 angstrom). Is it possible to 
change this tolerance (similar to setting DELTA within POINT GROUP when using 
CPMD), and if so what is the variable name?

I have looked through the FAQ and the variable list, and a little at the 
code, and think that this variable I am looking to change is tol8 from 
symatm.F90.

Any further assistance would be helpful.

Please find below the input file used.  I first attemped to send this from 
email, not the website, so formatting is a bit off from cutting and pasting 
from the rejected email.

Thank you,

Mark E. Kosmowski 
Department of Chemistry 
Syracuse University 
Syracuse, New York, USA

# K2ReH9 crystal, Inorg Chem, 1964, 558 # # In this input file, the location 
of the information on this or that line # is not important : a keyword is 
located by the parser, and the related # information should follow. # The "#" 
symbol indicate the beginning of a comment : the remaining # of the line will 
be skipped.
#Definition of the unit cell acell 2*9.607 5.508 angstrom # The keyword 
"acell" refers to the
# lengths of the primitive vectors (in Bohr) angdeg 2*90 120 spgroup 189 
#P-62m space group
#chkprim 0 # allows non-primitive unit cells #not needed for this run

#Definition of the atom types 

ntypat 3 # There are three types of atoms 
znucl 75 1 19 # 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. Re, H, K

#Definition of the atoms natom 36 # There are 36 atoms 
typat 3*1 27*2 6*3 # 3Re 27H 6K 

xred # This keyword indicate that the location of the atoms
# will follow, one triplet of numbers for each atom 

#Re
0.00000 0.00000 0.00000
0.33330 0.66670 0.50000
0.66670 0.33330 0.50000 
#H
0.17890 0.00000 0.00000
-0.17890 -0.17890 0.00000
0.00000 0.17890 0.00000
-0.12110 0.00000 0.21710
0.12110 0.12110 -0.21710
0.00000 -0.12110 0.21710
-0.12110 0.00000 -0.21710
0.12110 0.12110 0.21710
0.00000 -0.12110 -0.21710
0.14830 0.62500 0.50000
0.62500 0.14830 0.50000
0.47670 0.85170 0.50000
0.85170 0.47670 0.50000
0.37500 0.52330 0.50000
0.52330 0.37500 0.50000
0.22400 0.52540 0.71250
0.52540 0.22400 0.71250
0.30140 0.77600 0.28750
0.77600 0.30140 0.28750
0.47460 0.69860 0.71250
0.69860 0.47460 0.71250
0.22400 0.52540 0.28750
0.52540 0.22400 0.28750
0.30140 0.77600 0.71250
0.77600 0.30140 0.71250
0.47460 0.69860 0.28750
0.69860 0.47460 0.28750 
#K
0.00000 0.58810 0.00000
0.41190 0.41190 0.00000
0.58810 0.00000 0.00000
0.00000 0.26100 0.50000
0.26100 0.00000 0.50000
0.73900 0.73900 0.50000
#Definition of the planewave basis set 
ecut 10.0 # Maximal plane-wave kinetic energy cut-off, in Hartree

#DFT information 
ixc 11 #GGA PBE

#Definition of the k-point grid 
#nkpt 1 # Only one k point is needed for isolated system,
# taken by default to be 0.0 0.0 0.0
#Geometry optimization 
ionmov 2
#Definition of the SCF procedure nstep 50 # Maximal number of SCF cycles 
ntime 50 # number of time steps (opt steps) per SCF cylcle 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 1.0 # Although this is not mandatory, it is worth to
# precondition the SCF cycle. The model dielectric 
diemix 0.5 # function used as the standard preconditioner
# is described in the "dielng" input variable section.