[DFTB-Plus-User] Problems with supercell phonons calculation

[Alessandro LANDI]

Dear DFTB+ users, I have some problems concerning the evaluation of the
phonons of a supercell.
In particular I am working on a 2x2x1 supercell of Rubrene (1120 atoms).

1)  In order to get the phonons I first perform an optimization of the unit
cell with a 2x2x1 k-point sampling (see the bottom of this email for the
input code); then, starting from the optimized structure, I construct a
2x2x1 supercell and perform an optimization of the whole supercell with a
1x1x1 k-point sampling.
In other words, the input file is the same I used for the unit cell
optimization but for the k-point section.

 As expected, the starting structure is very near to the minimum of energy
and optimization (Maximal force component 10^-8) ends in less than 5
cycles. Let us call this optimized supercell  "supercell A" (picture not
atttached to avoid exceeding max dimensions of the message). Computation of
the Hessian and the modes for "supercell A" leads to a quite high number of
negative frequencies (up to 40), suggesting that the structure is not in
the real minimum of energy. Thus, I slightly distort the structure along
the lowest-frequency normal mode and restart the optimization, obtaining a
structure that we can refer to as "supercell B". Problem is, this time I
get a completely different structure from "supercell A": the molecules are
not equally spaced; on the contrary, they come closer to each other leaving
a quite big gap (see the image attached). Nevertheless, this time I get
positive frequencies, thus indicating that "supercell B" should be the real
minimum.

Is it normal? Since (I hope) I am working in Periodic Boundary Conditions,
I expect that replicating the optimized supercell in order to construct a
(virtually endless) crystalline structure I do not have gaps between the
repeating unit (which is the 2x2x1 supercell). Indeed, I would have no gaps
if I replicate the "supercell A" (which however leads to negative
frequencies), while I do have gaps in the "supercell B" which however
should be the correct one, having positive frequencies. What am I doing
wrong?

2) You can notice that I have "fragmented" molecules in the pictures
attached. This happens because I have used "ShowFoldedCoords=Yes" in the
input file and the starting geometry has some negative coordinates. Of
course, by setting"ShowFoldedCoords=No", I get molecules which are not
fragmented. However, in this case the 2x2x1 supercell obtained by
replicating the optimized unit cell (again with a 2x2x1 k-point sampling)
is quite far from the energy minimum (Maximal force component about 10^-3
at cycle 1). This is very different from what I obtained when
using "ShowFoldedCoords=Yes" (see my description at point 1) above), where
the 2x2x1 supercell was very near to the minimum of energy right from the
start.
 Is this  difference between two computations, differing only for
"ShowFoldedCoords", normal? I remark that the 2x2x1 supercell is simply
obtained by replicating the unit cell properly shifted by a displacement
equal to the lattice constants expressed in cartesian coordinates.
Taking advantage of the fact that the unit cell is orthorhombic in
pseudo-code it can be written as:
for i in range(2):
   for j in range(2):
    for k in range(1):
        x=x+i*a_axis
        y=y+j*b_axis
        z=z+k*c_axis


Thank you for any help you can give me
Best regards,
Alessandro

INPUT FILE:

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_3ob/"
    Separator = "-"
    Suffix = ".skf"
}
  MaxAngularMomentum = {
    H = "s"
    C = "p"
}
  Filling = Fermi {
     Temperature [Kelvin] = 300.0
  }
  KpointsAndWeights = SuperCellFolding {
    2 0 0
    0 2 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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