[DFTB-Plus-User] Slow Convergence problem

Ben Hourahine benjamin.hourahine at strath.ac.uk
Thu Aug 16 18:55:57 CEST 2012


Dear Bikash,

The "Lattice Step = 0" is the significant part. So far only the internal 
coordinates are optimising, but not the
lattice constants. Speaking as the author of these routines, the 
optimisation is nested with the structure

Optimise lattice vectors {
     Optimise internal coordinates{}
}

You could try setting no atoms to move ( MovedAtoms = {} ) as a first 
pre-relaxation (the pressure will certainly decrease then).

Regards

Ben


On 16/08/12 17:25, bikash sankar kanungo wrote:
> Dear Jan,
>
> Thanks for such a descriptive and insightful reply. I kept the 
> timestep =0.1 fs as the temperature of the system showed a sharp rise 
> for 1fs ultimately printing Nan. I made some trials and found 0.25fs 
> to be the the maximum timestep that worked for me.
>
>
> For my NPT(Berendsen thermostat and barostat) run in DFTB I did not 
> notice any pressure change after 100 geometry steps( = 10fs for a 
> timestep of 0.1fs). But since I have set Timescale=50fs so after 10fs 
> I expected some change in pressure. May be I am being too anxious 
> about my outputs.
>
> I am doing a LatticeOpt simultaneously , but strangely I never got 
> beyond Lattice Step = 0 for any of the 100 Geometry Steps I have 
> reached so far. Is that an expected behavior ?
>
> For the time being I will let them go upto 1000-2000 steps which may 
> take a week and see if I get any success else I will have to for a 
> smaller system and work out the re-scaling approach you suggested.
>
> Thank you,
> Bikash
>
> On Thu, Aug 16, 2012 at 8:51 PM, Jan M. Knaup 
> <Jan.Knaup at bccms.uni-bremen.de <mailto:Jan.Knaup at bccms.uni-bremen.de>> 
> wrote:
>
>     Dear Bikash,
>
>     50 fs is an extremely short simulation time, especially to get a
>     barostat to converge, especially at 10 K where the low temperature
>     naturally leads to very slow atomic movment. The first question to
>     ask would be, why do you use 0.1 fs time steps? For hydrocarbons
>     0.5 - 1.0 fs are usually sufficient at room temperature, let alone
>     at almost liquid helium temperature.
>
>     You do not write after how many geometry iterations you do not see
>     significant chage of the pressure, but from your NVP procedure, I
>     assume you check after a few hundred iterations. For a system with
>     that many atoms, that is not a lot.
>
>     As a general rule of thumb, conjugate gradient relaxation takes
>     about as many geometry steps as you have degrees of freedom in you
>     system. Of course this depends on the system and your convergence
>     criteria to some degree, still I would expect needing anywhere
>     between 1000 and 5000 steps for a system like yours, for geometry
>     relaxation at constant volume. Even small differences in the
>     equilibrium bond lengths between whatever force field you use and
>     the DFTB parameters you use can easily explain your pressure of
>     10^9 Pa. During the constant volume part of the CG relaxation,
>     drastic change of the pressure is very unlikely to occur since you
>     use a quite realistic model from your MM calculations.
>
>     You would have to perform an optimization of the lattice vectors
>     to arrive at a low pressure (Keyword LatticeOpt in the DFTB+
>     manual). However, the lattice optimization is performed in its own
>     loop outside the atomic configuration. That means, that for
>     lattice optimization, geometry optimizations at constant volume
>     are performed for different volumes and cell shapes. It can take
>     anywhere between 5 and 20 lattice steps, possibly even more. It is
>     very difficult to predict if you will need many geometry steps
>     after a change in the lattice vectors or not. This depends a lot
>     on the symmetry and rigidity of your system.
>
>     Unfortunately, there is not really any way around this procedure,
>     if you want to have your model at a pressure close to 1 atm.
>     However, it is probably possible to reduce the number of necessary
>     geometry and lattice iterations, even if you chose not to optimize
>     the DFTB cell volume:
>
>     You could take a much smaller model of maybe 150 atoms or
>     thereabouts, perform your LAMMPS procedure, then do a full
>     geometry and lattice optimization in DFTB. From that you can
>     obtain the equilibrium densities of your model for both
>     force-field and DFTB. If you then rescale the big model to obtain
>     the same volume ratio between LAMMPS output und DFTB+ input as for
>     the small model, that will likely save you a lot of geometry
>     iterations.
>
>     Hope this helps,
>
>     Jan
>
>     Jan M. Knaup                      | Fon +49-(0)421-218-62351
>     Dipl. Phys. Dr. rer. nat.         | Fax +49-(0)421-218-62770
>     Universität Bremen - BCCMS        |
>     Am Fallturm 1                     | Jan.Knaup at bccms.uni-bremen.de
>     <mailto:Jan.Knaup at bccms.uni-bremen.de>
>     28359 Bremen                      | JanKnaup at gmail.com
>     <mailto:JanKnaup at gmail.com>
>     Germany | www.bccms.uni-bremen.de <http://www.bccms.uni-bremen.de/>
>
>
>     2012/8/16 bikash sankar kanungo <biku.kanungo at gmail.com
>     <mailto:biku.kanungo at gmail.com>>
>
>         Hi,
>
>         Hi I am trying to relax an epoxy polymer matrix in DFTB . The
>         polymer matrix is obtained by cross-linking the epoxy monomers
>         with a curing agent. The cross-linking is done using Classical
>         MD tool LAMMPS. Before feeding the cross-linked structure(of
>         1322 atoms) from LAMMPS to DFTB I ensured to keep the pressure
>         to be 1 atm by doing NPT runs in LAMMPS. But while doing
>         structure relaxation in DFTB using Conjugate Gradient Driver I
>         do not see any change in order of magnitude of pressure which
>         remains as high as 1.0E+09 Pa. With a hope of reducing the
>         pressure to 1.0E05(1 atm) I even tried Verlocity Verlet using
>         Berendsen Thermostat and Barostat with target temperature =
>         10K , target pressure=1.0E+05 Pa , Timestep=0.1fs, Timescale =
>         50fs but the pressure still remains at around 1.0E+09 Pa even
>         after 10fs. To obtain SCC convergence I have set Broyden
>         mixing parameter = 0.3(default=0.2\0 and Fermi Fillinf
>         temperature=300K(default=0K). Do I need to provide more time
>         for convergence for such a large system or are there other
>         alternatives to boost the convergence rate?
>
>         I would appreciate any help or suggestions regarding the
>         relaxation of this seemingly difficult structure.
>
>         Thank you,
>         Bikash
>         -- 
>         BIKASH SANKAR KANUNGO
>         Final Year Undergraduate student,
>         Mechanical Engineering Department,
>         INDIAN INSTITUTE OF TECHNOLOGY
>         KHARAGPUR.
>         +919749935409 <tel:%2B919749935409>
>
>
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>
>
>
> -- 
> BIKASH SANKAR KANUNGO
> Final Year Undergraduate student,
> Mechanical Engineering Department,
> INDIAN INSTITUTE OF TECHNOLOGY
> KHARAGPUR.
> +919749935409
>

-- 
      Dr. B. Hourahine, SUPA, Department of Physics,
    University of Strathclyde, John Anderson Building,
           107 Rottenrow, Glasgow G4 0NG, UK.
     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
    The University of Strathclyde is a charitable body,
registered in Scotland, with registration number SC015263

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