Hi Zahra, Could you give us the input file so that we can identify the error properly? The error occurs because some of the atoms are very close to each other.
Regards, Juzar Thingna Department of Physics, Center for Computation Science and Engineering, National University of Singapore. On Mon, Apr 18, 2011 at 3:22 PM, zahra akbarinejad <[email protected] > wrote: > Hi siesta users > > When Siesta calculates the DM, in the output file the following warnings > appears: > To remove the warnings, I have repeatedly changed the unit cell > That means I bring up the unit cell to lattice vectors distance from the > edge atoms is much > But each time the following errors will appear > Can any one help me? > > siesta: WARNING: Atoms 5 46 too close: rij = 0.000003 Ang > siesta: WARNING: Atoms 6 48 too close: rij = 0.000003 Ang > siesta: WARNING: Atoms 9 114 too close: rij = 0.000008 Ang > siesta: WARNING: Atoms 10 116 too close: rij = 0.000008 Ang > siesta: WARNING: Atoms 11 162 too close: rij = 0.000011 Ang > siesta: WARNING: Atoms 12 164 too close: rij = 0.000011 Ang > siesta: WARNING: Atoms 13 218 too close: rij = 0.000016 Ang > siesta: WARNING: Atoms 14 220 too close: rij = 0.000016 Ang > siesta: WARNING: Atoms 45 46 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 47 48 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 113 114 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 115 116 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 161 162 too close: rij = 0.000002 Ang > siesta: WARNING: Atoms 163 164 too close: rij = 0.000002 Ang > siesta: WARNING: Atoms 217 218 too close: rij = 0.000004 Ang > siesta: WARNING: Atoms 219 220 too close: rij = 0.000004 Ang > siesta: WARNING: Atoms 253 294 too close: rij = 0.000003 Ang > siesta: WARNING: Atoms 254 296 too close: rij = 0.000003 Ang > siesta: WARNING: Atoms 257 362 too close: rij = 0.000008 Ang > siesta: WARNING: Atoms 258 364 too close: rij = 0.000008 Ang > siesta: WARNING: Atoms 259 410 too close: rij = 0.000011 Ang > siesta: WARNING: Atoms 260 412 too close: rij = 0.000011 Ang > siesta: WARNING: Atoms 261 466 too close: rij = 0.000016 Ang > siesta: WARNING: Atoms 262 468 too close: rij = 0.000016 Ang > siesta: WARNING: Atoms 293 294 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 295 296 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 361 362 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 363 364 too close: rij = 0.000000 Ang > siesta: WARNING: Atoms 409 410 too close: rij = 0.000002 Ang > siesta: WARNING: Atoms 411 412 too close: rij = 0.000002 Ang > siesta: WARNING: Atoms 465 466 too close: rij = 0.000004 Ang > siesta: WARNING: Atoms 467 468 too close: rij = 0.000004 Ang > New_DM. Step: 1 > Initializing Density Matrix... > > InitMesh: MESH = 384 x 384 x 64 = 9437184 > InitMesh: Mesh cutoff (required, used) = 100.000 107.843 Ry > > * Maximum dynamic memory allocated = 920 MB > Error in Cholesky factorisation in cdiag > ERROR STOP from Node: 0 > Error in Cholesky factorisation in cdiag > ERROR STOP from Node: 0 > > Thanks > >
