I guess your thin-film is too thin. What it says is that the atoms ia1 and ia2 are too close. In your case they are exactly the same atom. I would suspect one of you unit-cell parameters to be very small, or that your unit-cell is overpopulated with atoms.
Try and plot your structure using any software and see if two atoms are on top of each other. Then correct your structure to retain only the principal cell atoms. 2015-05-21 8:59 GMT+02:00 aouchenni boudjemaa <[email protected]>: > Hi siesta users, > I run a job for thin films, so it makes these errors. is there anyone ho > can give me a solution. > > siesta: WARNING: Atoms 5 7 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 6 7 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 12 14 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 13 14 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 19 21 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 20 21 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 26 28 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 27 28 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 33 35 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 34 35 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 40 42 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 41 42 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 47 49 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 48 49 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 54 56 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 55 56 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 61 63 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 62 63 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 68 70 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 69 70 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 75 77 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 76 77 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 82 84 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 83 84 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 89 91 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 90 91 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 96 98 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 97 98 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 103 105 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 104 105 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 110 112 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 111 112 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 117 119 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 118 119 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 124 126 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 125 126 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 131 133 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 132 133 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 138 140 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 139 140 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 145 147 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 146 147 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 152 154 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 153 154 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 159 161 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 160 161 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 166 168 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 167 168 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 173 175 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 174 175 too close: rij = 0.000000 Ang > New_DM. Step: 1 > Initializing Density Matrix... > > initdm: Initial spin polarization (Qup-Qdown) = 21.999999 > > InitMesh: MESH = 54 x 54 x 270 = 787320 > InitMesh: Mesh cutoff (required, used) = 500.000 503.697 Ry > > * Maximum dynamic memory allocated = 276 MB > Error in Cholesky factorisation in cdiag > Error in Cholesky factorisation in cdiag > ERROR STOP from Node: 0 > ERROR STOP from Node: 0 > > B.Aouchenni > PhD student > > -- Kind regards Nick
