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

[Bálint Aradi]

Dear Alessandro,

A few thoughts:

- When you optimize the molecule in the original supercell, do you also
allow the cell to relax? Otherwise you may still have stress in the
system, which has not be relaxed out. However, since you have only 1
molecule per supercell, there is no way to reduce the stress with fixed
lattice vectors. (If one molecule moves within the cell, all its
periodic images will move as well, keeping the distance between the
constant...)

- If the simple unit cell has been relaxed properly, there should be no
relaxations in the repeated cell at all, especially if the k-point
samplings are identical (in the sense, that considering the k-point
folding the enlarged supercell generates the same k-points as you have
used in the original cell.)

- I do not understand the reasoning about the differences when using
ShowFoldedCoords with Yes or No. If you have periodicity, folding the
coordinates should have no effect on any results. If you repeat the
supercell endlessly (which the periodic boundary conditions do), you
would get exactly the same system, whether you used the folded or
unfolded-coordinates.

Best regards,

Bálint



On 22.05.20 09:55, Alessandro LANDI wrote:
> 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
> 
> _______________________________________________
> 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
> 


-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/


-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: OpenPGP digital signature
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20200522/40ae30e5/attachment-0001.sig>