[DFTB-Plus-User] How DFTB+ manages atomic charges?
Bálint Aradi
aradi at uni-bremen.de
Tue Nov 22 14:43:53 CET 2022
> Being aware that charge transfer reactions should be treated with other
> methods, I am however trying to simulate the impact of different ions
> with a polymeric surface (at 300 K).
> Here's another issue: the runs are incredibly slow. This of course makes
> me think I'm doing something wrong.
> Can you please take a look and provide some tips to speed them up
> (besides increasing the core number) ?
> Please find attached an example of calculation, which performed only
> 17-18 steps in 24h.
Your system converges quite slowly for some reaons. I've raised the
temperature to 1000 K to ease convergence, set SccTolerance to he
default value, used the default (Broyden) mixer with the default
parameters. On my 6 years old laptop, I've managed so to run your system
for 10 geometry steps within 5 minutes and 12 seconds (using 4 threads)
with the serial Conda-binary, so I should be able to do ca. 3000 steps
per day.
If it is considerable slower for you, you are either using too many
threads/processes or your build is completely broken.
Best regards,
Bálint
>
> Many thanks
> Best regards
>
> Giacomo
>
> Il giorno mar 22 nov 2022 alle ore 11:50 Bálint Aradi
> <aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>> ha scritto:
>
> Just a quick note on this. Given the rather small size of our
> Hamiltonian (as compared to ab inito DFT calculations) and the fact,
> that we do not need to carry out integrations during the calculations,
> usually you don't gain much from running DFTB+ on multiple nodes with
> only a few hundreds of atoms. So please, always check the scalability
> (OpenMP threads or MPI processes) first and choose the number of
> threads
> or MPI processes accordingly. Otherwise you may end up with wasting
> computational resources and also your precious wall clock time.
>
> Best regards,
>
> Bálint
>
>
> On 17.11.22 14:19, giacomo buccella wrote:
> > Dear Charly,
> >
> > my sistem is nearly 350 atoms. It is not that big, but enough to
> be sort
> > of unaffordable without using parallel machines, since I need to run
> > tens of MD runs considering different starting configurations. I
> surely
> > can run one test with a single thread, just to check how much the
> result
> > is affected by using long-range corrections.
> > Many thanks for your support
> > Best regards
> >
> > Giacomo
> >
> > Il giorno gio 17 nov 2022 alle ore 14:13 Carlos R. Lien-Medrano
> > <cmedrano at uni-bremen.de <mailto:cmedrano at uni-bremen.de>
> <mailto:cmedrano at uni-bremen.de <mailto:cmedrano at uni-bremen.de>>> ha
> scritto:
> >
> > Dear Giacomo,
> >
> > I don't know the dimensions of your system but is it strictly
> needed
> > that you run
> > the calculation in parallel? Otherwise, you could give a chance
> > performing the
> > calculation just in one node using long-range corrections.
> >
> > Best regards,
> > Charly
> >
> > El jue, 17 nov 2022 a las 7:02, giacomo buccella
> > (<gek.buccella at gmail.com <mailto:gek.buccella at gmail.com>
> <mailto:gek.buccella at gmail.com <mailto:gek.buccella at gmail.com>>>)
> escribió:
> >
> > Dear Bálint,
> > thanks for the kind reply. I've just tried to implement Long
> > Range corrections, but it seems that this option is not yet
> > available when you run with mpi threads:
> >
> > **********************
> > ...
> > Starting initialization...
> >
> --------------------------------------------------------------------------------
> > WARNING!
> > -> Dipole printed for a charged system : origin dependent
> quantity
> > WARNING!
> > -> Dipole printed for extended system : value printed is not
> > well defined
> > ERROR!
> > -> Range separated calculations do not work with MPI yet
> >
> > *********************
> > Do you have any other advice?
> >
> > Many thanks
> > best regards
> >
> > Giacomo
> >
> > Il giorno gio 17 nov 2022 alle ore 07:54 Bálint Aradi
> > <aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>
> <mailto:aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>>> ha scritto:
> >
> > Dear Giacomo,
> >
> > this not DFTB related, but is common for all DFT
> approaches:
> > DFT(B)
> > methods tend to delocalize charges. You have one common
> > Fermi level in
> > the system, and if you have degenerated (or
> > quasi-degenerated) states,
> > such as likely the atomic level of the N atom and the
> VBM of
> > your
> > surface, charge will be distributed between them,
> > independently, how far
> > they are spatially from each other.
> >
> > Charge transfer reactions are usually calculated
> using range
> > separated
> > functionals (which you have in DFTB as well).
> Alternatively,
> > one can
> > also enforce a charge distribution via constraint
> DFT, but
> > we don't have
> > constrained DFTB in the official version yet.
> >
> > Best regards,
> >
> > Bálint
> >
> >
> > On 16.11.22 11:16, giacomo buccella wrote:
> > > Hi everyone, I'm asking for help about an issue to
> which
> > I don't find
> > > any answer in the manual.
> > > I'm interested in simulating a chemical system with
> > excess (or lack) of
> > > charge on certain particular atoms.
> > > The problem is that the after a single MD step
> > (timestep=0.5 fs), the
> > > charge is already delocalized among all atoms in the
> > cell. This occurs
> > > even if I'm simulating an ion approaching a
> distant surface.
> > >
> > > Example:
> > > I want to simulate the ion N(+) approaching a
> surface, so
> > I set the
> > > initial charge of N atom = +1.000 :
> > >
> > > InitialCharges = {
> > > AtomCharge = {
> > > Atoms = N
> > > ChargePerAtom = +1.0000
> > > }
> > > }
> > >
> > > therefore, I expect that at the beginning of the
> > simulation the number
> > > of electrons associated with N would be 5-1=4.
> > > Well, after a single MD step, its charge is
> already about
> > 4.9, even if
> > > it is still 10 AA away from other atoms in the system
> > with which it
> > > could interact.
> > >
> > > My question is: how is this possible? is it something
> > related to the way
> > > DFTB+ manages the charge distribution? Do I need a
> > time-dependent
> > > calculation for this?
> > > Any suggestion would be really appreciated
> > > Many thanks
> > >
> > > Giacomo
> > >
> > >
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> >
> > --
> > Dr. Bálint Aradi
> > Bremen Center for Computational Materials Science,
> > University of Bremen
> > http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/
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> >
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> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
>
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--
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/
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