[DFTB-Plus-User] How DFTB+ manages atomic charges?
giacomo buccella
gek.buccella at gmail.com
Tue Nov 22 14:24:22 CET 2022
Dear Bálint,
thank you for your kind reply.
Actually I have already checked for scalability on our machines, however I
am forced to use a reduced number of MPI threads (12 at most) for each
calculation. This because I'm experiencing the "sleeping state" issue
already (briefly) treated in another discussion. Unfortunately at the
moment I'm unable to install the conda version of dftb+ as you suggested,
hopefully I will give it a chance in the future.
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.
Many thanks
Best regards
Giacomo
Il giorno mar 22 nov 2022 alle ore 11:50 Bálint Aradi <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>> 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>>) 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>> 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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> --
> 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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