hi, the atom positions are incorrect. almost zero inter atomic distance means these 2 atoms are at the same position. for example atom 31 and 32 have almost same position.you can find more such pairs. please check your structure files.... you have 2 Cr atoms and 30 C atoms...is this what you want... s.auluck
> 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 >> >> > ....................................................................... Prof. Sushil Auluck Phone:+91-512-6797092/6148 Department of Physics +91-512-6798177(Home) Indian Institute of Technology Cell :+91-9305548667 Kanpur 208016 (UP) Fax :+91-512-6790914 India E-mail:[email protected] ...............................................:[email protected] http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html ....................................................................... ~
