[DFTB-Plus-User] Slow Convergence problem
Jan M. Knaup
Jan.Knaup at bccms.uni-bremen.de
Fri Aug 17 13:00:44 CEST 2012
Dear Bikash,
0.1 K ist definitely low enough. It is not unheard of that people just use
a snapshot from an MD at room temperature as the relaxation starting point.
>From your careful procedure I was quite sure you did not do that, but I
wanted to be certain.
Best,
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
28359 Bremen | JanKnaup at gmail.com
Germany | www.bccms.uni-bremen.de
2012/8/17 bikash sankar kanungo <biku.kanungo at gmail.com>
> 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
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at dftb-plus.info
> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
>
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