[DFTB-Plus-User] Fragmented optimized structure

[Alessandro LANDI]

Dear DFTB+ users,
I have performed a geometry optimization of a supercell in Cartesian
coordinates (S in header of the gen file). I provide the input I have used
at the end of this email.

However, even though the starting geometry consists of 4 molecules
"connected", the optimized geometry is formed by disconnected fragments. I
am aware that this is due to the periodicity of the calculation, and indeed
the optimized atom coordinates are similar to the starting ones plus or
minus the supercell vectors provided in the gen format.

Problem is, I need to reconstruct the "connected" molecules starting from
the fragments obtained after the optimization, to perform other
calculations on them. Does the DFTB+ suite provide a utility to do this?

Thank you for your help.

Best regards,
Alessandro

P.S. Here is the input I am using:


*Geometry = GenFormat {<<< "geom_start.gen"}*





















































*Driver = ConjugateGradient {  MovedAtoms = 1:-1  MaxForceComponent = 1E-8
MaxSteps = 10000  LatticeOpt = No  OutputPrefix = "geom_opt"}Hamiltonian =
DFTB {  SCC = Yes  SCCTolerance = 1e-10  MaxSCCIterations = 20000  Mixer =
Broyden {    MixingParameter = 0.99}  SlaterKosterFiles = Type2FileNames{
  Prefix = "Slako/" #If it is in a different directory, put the path
Separator = "-"    Suffix = ".skf"}  MaxAngularMomentum = {    H = "s"    C
= "p"}  Filling = Fermi {     Temperature [Kelvin] = 300.0  }
KpointsAndWeights = SuperCellFolding {    1 0 0    0 1 0    0 0 1    0.0
0.0 0.0}  Eigensolver = DivideAndConquer {}  Differentiation = Richardson
{}  ThirdOrderFull = Yes  DampXH = Yes  DampXHExponent = 4.0  HubbardDerivs
{   H = -0.1857   C = -0.1492}  Dispersion = DftD3{}*










*}Options {ShowFoldedCoords       =       Yes}Parallel {  UseOmpThreads =
Yes} ParserOptions = {  ParserVersion = 5}*


-- 
Alessandro Landi, Assegnista di Ricerca
Dipartimento di Chimica e Biologia "Adolfo Zambelli"
Università degli Studi di Salerno
Via Giovanni Paolo II, 132 - 84084 - Fisciano (SA)
Phone number 089969390
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