[DFTB-Plus-User] How DFTB+ manages atomic charges?
giacomo buccella
gek.buccella at gmail.com
Tue Nov 22 15:06:38 CET 2022
Ok, thank you very much for your help and patience.
Best regards
Giacomo
Il giorno mar 22 nov 2022 alle ore 15:03 Bálint Aradi <aradi at uni-bremen.de>
ha scritto:
> On 22.11.22 14:48, giacomo buccella wrote:
> > I'll with default mixer then, but what about the temperature? Why should
> > I increase it up to 1000 K when I want reaction dynamics at 300K?
>
> Because, this is the electronic temperature, not the ionic one, so its
> OK to have a different value from the actual ambient temperature.
> Consider it more as a tool to help you accelerating convergence. As long
> as it is not too high, the results should be OK. Your system will also
> converge with 300 K electronic temperature, but will need much more
> SCC-cycles. I doubt, that there will be a significant difference in the
> trajectories, though, but you should maybe test it.
>
> By the way, the convergence may become smoother, when the system has
> done a few steps already. If you are concerned about the high electronic
> temperature, do a few steps with it and restart then the MD with a lower
> one from there.
>
> One more remark: on my laptop the optimal nr. of threads is 2, I finish
> the same calculation in less than 4 minutes then. Your system is just
> too small to scale beyond 2 threads, so make sure, you do not run it on
> too many threads/cores. Make sure to set OMP_NUM_THREADS and/or the
> 'mpirun -n' parameter correctly.
>
> Best regards,
>
> Bálint
>
>
> >
> > Il giorno mar 22 nov 2022 alle ore 14:44 Bálint Aradi
> > <aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>> ha scritto:
> >
> >
> > > 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>
> > <mailto: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>>
> > > <mailto: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>>
> > > <mailto: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>>
> > > <mailto: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/>
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> > > >
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> > > >
> > > >
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> > > >
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> > >
> > > --
> > > Dr. Bálint Aradi
> > > Bremen Center for Computational Materials Science, University
> > of Bremen
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> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
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