this is my input
# General System descriptors
SystemLabel CrC6 # Short name for naming files
NumberOfAtoms 32 # Number of atoms
NumberOfSpecies 2 # Number of species
%block Chemical_Species_Label
1 24 Cr
2 6 C
%endblock Chemical_Species_Label
# Lattice, coordinates, k-sampling
LatticeConstant 1 Ang
%block LatticeParameters
4.36 4.36 7.12 90.0000 90.0000 60.0000
%endblock LatticeParameters
AtomicCoordinatesFormat NotScaledCartesianAng
AtomicCoordinatesFormatout Ang
%block AtomicCoordinatesAndAtomicSpecies
-0.00126 2.51135 5.34 1
2.17384 1.25556 1.780 1
2.89804 0.00049 3.56 2
-1.45035 2.51111 3.56 2
0.72391 1.25580 3.56 2
2.89901 0.00001 0.000 2
-1.46319 2.50752 0.0000 2
0.71980 1.24675 0.0000 2
1.43946 0.00037 3.56 2
-0.72111 1.24781 3.56 2
1.45339 2.51930 3.56 2
1.44005 -0.00278 0.000 2
-0.72241 1.24573 0.000 2
1.45217 2.51531 0.000 2
3.60730 1.25574 0.000 2
2.89901 2.51111 0.0000 2
3.60730 1.25574 3.56 2
2.89901 2.51111 3.56 2
-0.76553 3.76019 0.00000 2
0.72048 3.79475 0.00000 2
-0.76553 3.76019 3.56 2
0.72048 3.79475 3.56 2
2.89901 0.00001 7.12 2
-1.46319 2.50752 7.12 2
0.71980 1.24675 7.12 2
1.44005 -0.00278 7.12 2
-0.72241 1.24573 7.12 2
1.45217 2.51531 7.12 2
3.60730 1.25574 7.12 2
2.89901 2.51111 7.12 2
-0.76553 3.76019 7.12 2
0.72048 3.79475 7.12 2
%endblock AtomicCoordinatesAndAtomicSpecies
kgrid_cutoff 7. Ang
XC.functional GGA
PAO.EnergyShift 0.0025 Ry
PAO.SplitNorm 0.30
PAO.SplitNormH 0.50
ElectronicTemperature 0 K
DM.MixingWeight 0.30
DM.NumberPulay 5
MD.TypeofRun CG
MD.VariableCell true
MD.NumCGsteps 100
MD.MaxForceTol 0.01 eV/Ang
MD.MaxStressTol 200 bar
# DFT, Grid, SCF
Diag.ParallelOverK F
XC.functional GGA # Exchange-correlation functional type
XC.authors PBE # Particular parametrization of xc
func
SpinPolarized .True. # Spin unpolarized calculation
# Output options
WriteCoorInitial
WriteCoorStep .true.
WriteForces .true.
WriteKpoints .true.
WriteEigenvalues .true.
WriteKbands .true.
WriteBands .true.
WriteMullikenPop 1 # Write Mulliken Population Analysis
WriteCoorXmol .true.
WriteMDCoorXmol .true.
WriteMDhistory .true.
and this the error
siesta: ==============================
Begin CG move = 0
==============================
outcoor: Atomic coordinates (Ang):
-0.00126000 2.51135000 5.34000000 1 1 Cr
2.17384000 1.25556000 1.78000000 1 2 Cr
2.89804000 0.00049000 3.56000000 2 3 C
-1.45035000 2.51111000 3.56000000 2 4 C
0.72391000 1.25580000 3.56000000 2 5 C
2.89901000 0.00001000 0.00000000 2 6 C
-1.46319000 2.50752000 0.00000000 2 7 C
0.71980000 1.24675000 0.00000000 2 8 C
1.43946000 0.00037000 3.56000000 2 9 C
-0.72111000 1.24781000 3.56000000 2 10 C
1.45339000 2.51930000 3.56000000 2 11 C
1.44005000 -0.00278000 0.00000000 2 12 C
-0.72241000 1.24573000 0.00000000 2 13 C
1.45217000 2.51531000 0.00000000 2 14 C
3.60730000 1.25574000 0.00000000 2 15 C
2.89901000 2.51111000 0.00000000 2 16 C
3.60730000 1.25574000 3.56000000 2 17 C
2.89901000 2.51111000 3.56000000 2 18 C
-0.76553000 3.76019000 0.00000000 2 19 C
0.72048000 3.79475000 0.00000000 2 20 C
-0.76553000 3.76019000 3.56000000 2 21 C
0.72048000 3.79475000 3.56000000 2 22 C
2.89901000 0.00001000 7.12000000 2 23 C
-1.46319000 2.50752000 7.12000000 2 24 C
0.71980000 1.24675000 7.12000000 2 25 C
1.44005000 -0.00278000 7.12000000 2 26 C
-0.72241000 1.24573000 7.12000000 2 27 C
1.45217000 2.51531000 7.12000000 2 28 C
3.60730000 1.25574000 7.12000000 2 29 C
2.89901000 2.51111000 7.12000000 2 30 C
-0.76553000 3.76019000 7.12000000 2 31 C
0.72048000 3.79475000 7.12000000 2 32 C
superc: Internal auxiliary supercell: 7 x 7 x 4 = 196
superc: Number of atoms, orbitals, and projectors: 6272 82320 100352
outcell: Unit cell vectors (Ang):
4.360000 0.000000 0.000000
2.180000 3.775871 0.000000
0.000000 0.000000 7.120000
outcell: Cell vector modules (Ang) : 4.360000 4.360000 7.120000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 60.0000
outcell: Cell volume (Ang**3) : 117.2151
siesta: WARNING: Atoms 3 1398 too close: rij = 0.018550 Ang
siesta: WARNING: Atoms 4 210 too close: rij = 0.010640 Ang
siesta: WARNING: Atoms 6 4727 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 7 4728 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 8 4729 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 9 1397 too close: rij = 0.029701 Ang
siesta: WARNING: Atoms 10 209 too close: rij = 0.032570 Ang
siesta: WARNING: Atoms 12 4730 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 13 4731 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 14 4732 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 15 4733 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 16 4734 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 17 42 too close: rij = 0.032570 Ang
siesta: WARNING: Atoms 18 36 too close: rij = 0.010640 Ang
siesta: WARNING: Atoms 19 4735 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 20 4736 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 21 425 too close: rij = 0.029701 Ang
siesta: WARNING: Atoms 22 419 too close: rij = 0.018550 Ang
siesta: WARNING: Atoms 23 1574 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 24 1575 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 25 1576 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 26 1580 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 27 1581 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 28 1582 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 29 1583 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 30 1584 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 31 1587 too close: rij = 0.000000 Ang
siesta: WARNING: Atoms 32 1588 too close: rij = 0.000000 Ang
On Fri, Sep 13, 2013 at 12:51 PM, Sonu Kumar <[email protected]> wrote:
> waring of too close atom ,,here is my fdf file plz help me out
>>
>
> clearly you have defined your atoms to be close to each other.
>
> Check with the xcrysden and any other visualization software.
>
> Further, how many formula units of CrC6 are there in your hexagonal
> cell ?
>
> Also, it's better if you paste your input file rather than attaching it.
>
> hope it helps.
>
> regards,
> sonu
> IITD
>
>
