[DFTB-Plus-User] Hessian calculations and time limit
Alessandro LANDI
alelandi1 at unisa.it
Mon Feb 24 18:46:56 CET 2020
Thanks for the suggestions.
One last question: you said " Check that DFTB is using all the cores, you
are using OpenMP (Parallel>UseOMP = Yes) so you might not be."
Should I not use this feature? Should I set something different in the
input to be sure all the cores are used?
Thanks again.
Alessandro
Il Lun 24 Feb 2020, 18:16 Mat Toliday via DFTB-Plus-User <
dftb-plus-user at mailman.zfn.uni-bremen.de> ha scritto:
> That looks quite normal, the Hamiltonian>Mixer mixing parameter in the
> dftb_in.hsd file might be a bit large, you could try using the default
> value and you could try reducing the SCCtolerance to 1e-8. It should still
> work and may be a little faster but I don't think this will speed up
> calculation enough. Check that DFTB is using all the cores, you are using
> OpenMP (Parellel>UseOMP = Yes) so you might not be.
> Yours,
> Mat
> On Monday, 24 February 2020, 17:02:55 CET, Alessandro LANDI <
> alelandi1 at unisa.it> wrote:
>
>
> Hello,
> thank you for your reply. I have attached the input file I am using for
> Hessian calculation. I am using the values a senior researcher in my group
> suggested me (can you please check the attached file and tell me if you
> think they are too strict?)
>
> In particular I set SCCTolerance = 1e-10. Each geometry step requires
> 11-15 iSCC cycles, if I understand the output correctly (I reproduce part
> of the output in the following)
>
> *** Geometry step: 150
> iSCC Total electronic Diff electronic SCC error
> 1 -0.13686329E+04 0.00000000E+00 0.21400324E-04
> 2 -0.13686329E+04 0.91858965E-10 0.21229086E-04
> 3 -0.13686329E+04 0.72759576E-11 0.11813509E-04
> 4 -0.13686329E+04 -0.97543307E-10 0.30138133E-05
> 5 -0.13686329E+04 -0.21145752E-10 0.74044473E-06
> 6 -0.13686329E+04 -0.47748472E-11 0.24149976E-06
> 7 -0.13686329E+04 -0.45474735E-12 0.14577856E-06
> 8 -0.13686329E+04 -0.68212103E-12 0.38308579E-07
> 9 -0.13686329E+04 0.68212103E-12 0.16315258E-07
> 10 -0.13686329E+04 -0.45474735E-12 0.57164407E-08
> 11 -0.13686329E+04 0.22737368E-12 0.21716895E-08
> 12 -0.13686329E+04 0.00000000E+00 0.70770501E-09
> 13 -0.13686329E+04 -0.22737368E-12 0.25188207E-09
> 14 -0.13686329E+04 -0.22737368E-12 0.10402701E-09
> 15 -0.13686329E+04 0.45474735E-12 0.31696423E-10
> Total Energy: -1328.7955553888 H -36158.3668 eV
> Total Mermin free energy: -1328.7955553888 H -36158.3668 eV
> Volume: 0.752806E+05 au^3 0.111554E+05 A^3
> Pressure: -0.398475E-04 au -0.117235E+10 Pa
>
> Best regards,
> Alessandro
>
> Il giorno lun 24 feb 2020 alle ore 16:51 Mat Toliday via DFTB-Plus-User <
> dftb-plus-user at mailman.zfn.uni-bremen.de> ha scritto:
>
> Hello,
> As far as I know you can not restart the second derivatives calculation.
> However, the Hessian matrix is formed by shifting each atom in the positive
> and negative Cartesian directions and calculating the force. The matrix
> equation is: F_i = H_ij * d_j, where F is force, H is a second derivative,
> d a small displacement and i and j are indices for the degrees of freedom.
> If you were to add your delta value to an atomic coordinate and then
> calculated the force vector you could then calculate the Hessian entries
> yourself using H_ij = F_i/d_j. You should probably use central finite
> differences, calculating the forces for both + and - d_j values and
> calculate the difference using the forces from the relaxed unit cell. As
> far as I can tell this is what the SecondDerivatives driver does.
> I am a little surprised it is taking too long, what sccTolerance are you
> using and how many SCCcycles does each step take?
> Yours,
> Mat
>
> On Monday, 24 February 2020, 11:17:43 CET, Alessandro LANDI via
> DFTB-Plus-User <dftb-plus-user at mailman.zfn.uni-bremen.de> wrote:
>
>
> Dear DFTB+ users,
> I am trying to calculate the normal modes for a supercell of rubrene
> crystal, consisting of 1120 atoms. I have optimized the supercell and now I
> am computing the Hessian using in the input:
>
> Driver = SecondDerivatives {
> Atoms = 1:-1
> Delta = 1E-5
> }
>
> Problem is, I am working on a remote pc where calculations cannot last
> more than three days and it seems that, even using up to 80 cores, it is
> not enough to finish the hessian calculation in time.
> In light of this problem, I am wondering :
> 1) Is it possible to evaluate the second derivatives in more than one run?
> (Like the geometry optimization where I can run a subsequent calculations
> starting from the last geometry of the previous calculation...)
> 2) If this is not possible, can you suggest me another workaround to solve
> this problem?
>
> Thank you for any help you can give me
>
> Best regards,
> Alessandro
>
> --
> 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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>
>
> --
> 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
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