Hello again, Thank you all once again for the help.
Best wishes, Arturo Toro On Thu, Aug 18, 2016 at 2:52 PM, Andrei Postnikov < [email protected]> wrote: > Hi Arturo, > > you defined > *AtomicCoordinatesFormat Fractional* > so 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 out > which geometry you really want to use (how long the translation vectors > and where are the atoms in the cell: placed from one another > at distance =1.0 in which units?) > > Good luck > > Andrei Postnikov > > > ----- Arturo Toro <[email protected]> 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 > > >
