[DFTB-Plus-User] Slow Convergence problem
bikash sankar kanungo
biku.kanungo at gmail.com
Fri Aug 17 12:37:18 CEST 2012
Dear Jan and Ben ,
I am really grateful to you two for such valuable suggestions.
@Jan : I will continue my full geometry optimization till 1500-2000
geometry steps and see if I get any significant pressure change. Till now
the full geometry optimization which has reached to 200 geometry shows a
pressure fluctuation from 1.0E+07 to 1.0E+08 which at the start was around
1.0E+09 . So hopefully it will take some more time to hit the relaxed
geometry. I had previously done some benchmark testing regarding
bond-lengths and bond-angles of simple molecules (methane, ethylene
diamine) in both VASP and DFTB and found that feeding VASP optimized
structure to DFTB ( or vice-versa) showed large forces on few atoms and
high value of pressure which I suppose hints at stiff covalent bonds of
such molecules and for the same reason DFTB may not be liking my
force-fields from LAMMPS( class2/pcff).
In MD I cannot set the target temperature to be 0K so I had done my NVT/NPT
runs in LAMMPS at 0.1K . Is that low enough or do I need an even lower
order target temperature ? They reason for not going for too small value of
target temperature was that it would have constrained my atom movements
which could have caused a longer timescale for achieving the target
pressure.
@Ben : I will also degrade my force convergence criterion and try the
alternative proposed be you and look for any significant boost in
convergence.
Thank you,
Bikash
On Fri, Aug 17, 2012 at 3:09 PM, Benjamin Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:
> Dear Bikash,
>
> what you could try is to change the tolerance for the forces to be a poor
> quality
> and relax both the coordinates and lattice simultaneously using something
> like
> MaxForceComponent = 0.1
> and then repeat at tighter tolerances, eventually keeping the lattice
> fixed and just relaxing
> the internal coordinates precisely.
>
> Regards
>
> Ben
>
> ________________________________________
> From: dftb-plus-user-bounces at dftb-plus.info [
> dftb-plus-user-bounces at dftb-plus.info] On Behalf Of bikash sankar kanungo
> [biku.kanungo at gmail.com]
> Sent: 17 August 2012 08:37
> To: User list for DFTB+ related questions
> Subject: Re: [DFTB-Plus-User] Slow Convergence problem
>
> Dear Ben,
>
> Thanks for the help. By keeping all the atoms fixed and allowing the
> lattice constants to change I was able to reduce the pressure and achieve
> convergence in 24 geometry step( for fixed atoms case geometry steps and
> lattice step has same meaning). But feeding the end geometry for internal
> coordinates optimization starts with low pressure(1.0E+05) in the 0th
> geometry step and then shoots to 1.0E+09 in the next.
>
> Moreover,if I try a full geometry optimization(moved atoms+lattice opt)
> with the end geometry from fixed atoms lattice optimization it still
> performs only lattice step 0 and doesn't go beyond it.
>
> I suppose I will have to perform several the fixed atoms lattice
> optimization and then internal coordinates optimization(for about 100
> geometry steps) alternatively to achieve the relaxed structure.
>
>
> Thank you,
> Bikash
>
> On Thu, Aug 16, 2012 at 10:25 PM, Ben Hourahine <
> benjamin.hourahine at strath.ac.uk<mailto:benjamin.hourahine at strath.ac.uk>>
> wrote:
> 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<mailto:
> 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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>
>
>
>
> --
> BIKASH SANKAR KANUNGO
> Final Year Undergraduate student,
> Mechanical Engineering Department,
> INDIAN INSTITUTE OF TECHNOLOGY
> KHARAGPUR.
> +919749935409
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at dftb-plus.info
> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
--
BIKASH SANKAR KANUNGO
Final Year Undergraduate student,
Mechanical Engineering Department,
INDIAN INSTITUTE OF TECHNOLOGY
KHARAGPUR.
+919749935409
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