Hi Arturo, you definedAtomicCoordinatesFormat Fractionalso that your atoms Nr 1 and 2 %block AtomicCoordinatesAndAtomicSpecies 4.00 0.00 1.00 3 3.00 0.00 1.00 3 as well as many others, are at identical positions. You know, in "fractional" arithmetics 4=3 (=2=1=0)You can see this explicitly as the coordinates are printed in Bohr: siesta: Atomic coordinates (Bohr) and species siesta: 152.22128 0.00000 10.12043 3 1 siesta: 114.16596 0.00000 10.12043 3 2 - these coordinates are separated by exactly the 1st translation vector(20.138 Ang).Indeed, this is because of periodicity (which is implicit in Siesta),however this is not an error but exactly the structure as you decribed it...The first step in solving the problem would be to figure outwhich geometry you really want to use (how long the translation vectorsand where are the atoms in the cell: placed from one another at distance =1.0 in which units?) Good luckAndrei Postnikov----- Arturo Toro <lart1...@gmail.com> a écrit : >Hi all,
While attempting to run a molecular dynamics simulation of an interface between a hexagonal system and a cubic system, I received the above mentioned error message. I then looked through the .out file and saw that there were numerous atoms which, although visibly located at different atoms, are said to be 0 angstroms apart. I believe this to be the result of an innate periodicity function within SIESTA. Is there a way to avoid this error besides manually attempting to delete all the conflicting atoms? Thanks again, Arturo Toro
