[DFTB-Plus-User] Fragmented optimized structure

Sharma SRK Chaitanya Yamijala sharmajncasr at gmail.com
Fri May 1 22:59:57 CEST 2020


Hi Alessandro,

If you just need to get the fragments to be united, you can use VMD's PBC
option.

To visualize "all" the frames in your optimization trajectory, use the
below. You can also use the below settings even when you have a single
frame.

pbc set {10. 20. 15. 90. 90. 90.} -all; # a b c alpha beta gamma
pbc wrap -center unitcell -compound fragment -all; # For combining the
fragments.
pbc box; # If you want to display the periodic box

HTH,
Thanks,
Sharma.

--------------------------------------------------------------------
SRK *Chaitanya* Sharma, Yamijala.
https://scholar.google.com/citations?hl=en&user=IglNkREAAAAJ



On Fri, May 1, 2020 at 3:45 AM Alessandro LANDI via DFTB-Plus-User <
dftb-plus-user at mailman.zfn.uni-bremen.de> wrote:

> 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:
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> *Geometry = GenFormat {<<< "geom_start.gen"}*
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> *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{}*
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> *}Options {ShowFoldedCoords       =       Yes}Parallel {  UseOmpThreads =
> Yes} ParserOptions = {  ParserVersion = 5}*
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> --
> 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
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
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