[DFTB-Plus-User] Slow Convergence problem
Benjamin Hourahine
benjamin.hourahine at strath.ac.uk
Fri Aug 17 11:39:27 CEST 2012
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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INDIAN INSTITUTE OF TECHNOLOGY
KHARAGPUR.
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BIKASH SANKAR KANUNGO
Final Year Undergraduate student,
Mechanical Engineering Department,
INDIAN INSTITUTE OF TECHNOLOGY
KHARAGPUR.
+919749935409
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