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[Nuno Galamba <ngalamba@cii.fc.ul.pt>]

Hi 

I am doing NVE MD so I am not using the Nose thermostat. Total energy is the 
sum of kinetic energy of the nucleous plus the potential energy which has 
different terms (electronic, electron-nucleous, Ewald sum,...). The sum of 
the kinetic and potential energy is conserved up to 5 digits for the first 
~150 steps then it is lost, because the electronic energy stops converging 
(50 SCF cycles are not enough, while normaly 10-15 are enough for convergence 
to be reached during the first ~150 steps). At this point, looking at the 
positions one can see that there's an ion out of the supercell boundaries. I 
would think that periodic boundary conditions would prevent this from 
happening unless the time-step was too large. I am using 5fs which I would 
think is reasonable. Perhaps I am wrong?

Thanks

Best regards

Nuno Galamba


On Monday 26 September 2005 22:56, Mustafa Uludogan wrote:
> Hi,
> How do you define total energy or how is it defined?
> In terms of MD calculations, energies that you need to
> focus only on  electron-ion energy and  kinetic
> energy, not to the contributions from the Nose
> thermostat.
> Mustafa Uludogan
>
> --- ngalamba@cii.fc.ul.pt wrote:
> > Dear ABINIT users
> >
> > (Thanks for you answer to my first question Anglade)
> >
> > In fact the problem I have runned into in my MD
> > simulations of ionic systems (NaCl) is that after a
> > number of time-steps (about 150) the total energy
> > stops being conserved and
> > the energy does not converge (even within 50 SCF
> > cycles). At first I thought
> > this may had something to do with the way I was
> > linking the partial runs, but
> > now I am positive it does not as it should. In fact
> > the differences I
> > describe are only a matter of my energy convergence
> > tolerance as it is
> > normal.
> >
> > I notice that when convergence is not achieved and
> > the total energy is lost a
> > particle comes out the boundary of my supercell,
> > i.e. xcart > acell in one or
> > two space dimensions.
> >
> > I have been trying different time-steps and energy
> > tolerances but without much
> > success. Perhaps anyone could suggest me possible
> > causes for this behaviour.
> > Below its my my complete input file. I am using the
> > LDA Troullier-Martins
> > pseudopotentials.
> >
> > Maybe I am just doing something terribly wrong and
> > did not notice.
> >
> > Thanks in advance
> >
> >
> > Nuno Galamba
> >
> >
> >
> > INPUT FILE:
> >
> >
> > #Definition of the unit cell
> > acell 3*24.76786
> >
> > ixc 1             # Integer for eXchange-Correlation
> > choice
> >                   # 1=> LDA or LSD, Teter Pade
> > parametrization
> >                   # 11=> GGA, Perdew-Burke-Ernzerhof
> > GGA functional
> >
> > #Definition of the atom types
> > ntypat 2          # There are two types of atom
> > znucl 11 17       # The keyword "znucl" refers to
> > the atomic number of the
> >                   # possible type(s) of atom. The
> > pseudopotential(s)
> >                   # mentioned in the "files" file
> > must correspond
> >                   # to the type(s) of atom. There
> > are two types, Na and Cl.
> >
> > #Definition of the atoms
> > natom 64           # There are 64 atoms
> >                    # Na is type 1 Cl is type 2
> > typat 1 1 1 1 1 1 1 1
> >       1 1 1 1 1 1 1 1
> >       1 1 1 1 1 1 1 1
> >       1 1 1 1 1 1 1 1
> >       2 2 2 2 2 2 2 2
> >       2 2 2 2 2 2 2 2
> >       2 2 2 2 2 2 2 2
> >       2 2 2 2 2 2 2 2
> >
> > xcart              # This keyword indicate that the
> > location of the atoms
> >                    # will follow, one triplet of
> > number for each atom
> >   5.65610083276636E+00  6.93007271203097E+00
> >  3.98004166996406E+00
> >  -1.58868622079202E+00  2.63595639332169E-01
> >  5.57671342725475E+00
> >  -1.49430205342578E+00  8.27373084310587E+00
> >  4.28663901715516E+00
> >   6.20932440764681E+00  6.19744320361232E-01
> >  3.81901561805629E+00
> >   1.66283625121153E+01  5.40662784441812E+00
> >  6.76384828606851E+00
> >   1.19212420178225E+01  1.74664875846193E+00
> >  8.84595707944380E+00
> >   1.36798041986300E+01  5.19789720677238E+00
> >  1.18842635240986E+00
> >   1.57698075022031E+01 -2.47088396806683E+00
> >  1.71827272598309E+00
> >   8.82385488253922E+00  1.93800507464858E+01
> >  8.03045840728254E+00
> >  -2.96940590475408E-01  1.43296676103769E+01
> >  7.94873369769508E+00
> >   2.75193713439659E+00  1.66809052988040E+01
> >  2.21186590278981E+00
> >   5.75064910174398E+00  1.11428516068944E+01
> > -1.19206927353112E+00
> >   1.78970548725394E+01  1.96098850528562E+01
> >  8.36735017031766E+00
> >   1.32951507724950E+01  1.30273516304540E+01
> >  8.66302964244192E+00
> >   1.09075464378747E+01  1.74430765618708E+01
> > -7.18628166590436E-01
> >   1.79309814303632E+01  1.32659758625039E+01
> >  2.78007618501099E+00
> >   2.01757826162747E+00  3.70882481536942E+00
> >  2.13777333539610E+01
> >   5.45781986810109E-01 -8.53595129266538E-01
> >  1.58192342348621E+01
> >   2.58739506332547E+00  8.57151174405726E+00
> >  1.16833167489726E+01
> >   6.31615279367772E+00  3.21631280617979E+00
> >  1.48884408706589E+01
> >   1.80911588944757E+01  3.96995354871461E+00
> >  2.15402530489654E+01
> >   1.03525180976381E+01 -1.06550027411973E+00
> >  2.04211691806326E+01
> >   1.37565960570218E+01  5.51216185937855E+00
> >  1.52867729052235E+01
> >   1.74905236377205E+01  2.79139073706610E-01
> >  1.22055002724973E+01
> >   6.06615778959029E+00  1.87655731011766E+01
> >  1.71278047467966E+01
> >   3.27913887860641E-01  1.41249716583982E+01
> >  1.71225139608150E+01
> >   2.32242959524589E+00  2.04172925233845E+01
> >  1.12789799054557E+01
> >   8.64607887529689E+00  1.20514391946926E+01
> >  1.71318269534357E+01
> >   1.96817656859490E+01  1.93523059315386E+01
> >  1.86473997160438E+01
> >   1.64319052040267E+01  1.24034827539144E+01
> >  1.83563535673751E+01
> >   1.31683971038350E+01  2.05498272275597E+01
> >  1.41933514996297E+01
> >   1.86645236989813E+01  1.04990490908508E+01
> >  1.24197018270058E+01
> >  -3.44974273400398E-01  3.39183432946808E+00
> >  1.26158860130092E+00
> >   1.21850776103177E+00  5.38621021103299E+00
> >  7.27867587909737E+00
> >   6.71668083259319E+00 -3.04893236900015E-01
> >  9.19282809484037E+00
> >   5.52626261040444E+00  6.68068005936578E+00
> > -1.33470871179536E+00
> >   1.10729252318763E+01  7.34629036967786E-01
> >  1.38425105592482E+00
> >   1.22420458091739E+01  5.42730478887774E+00
> >  5.64406749630738E+00
> >   1.64808041637378E+01  1.04623190409022E-01
> >  7.05990714953118E+00
> >   1.81489484769993E+01  5.44020577061157E+00
> >  1.48758605236480E+00
> >  -1.00712948377719E+00  1.30466527849894E+01
> >  3.24896054062410E+00
> >   2.85687073048752E+00  1.87221152967594E+01
> >  6.64479963145403E+00
> >   6.18553802180375E+00  1.13751327461171E+01
> >  3.94029445346575E+00
> >   6.81250206482103E+00  2.00454488296633E+01
> >  3.00772892811612E-02
> >   1.54649514651704E+01  1.38577538331537E+01
> > -1.98271195022125E+00
> >   1.27794240773162E+01  1.74400126309805E+01
> >  7.94295780064528E+00
> >   1.73868429705585E+01  1.05386873127956E+01
> >  6.32376714120894E+00
> >   1.97748603591924E+01  1.85203159628838E+01
> >  3.55269786882534E+00
> >  -1.77300902536039E+00 -1.05286467903429E+00
> >  9.76102740263670E+00
> >  -2.87794597891296E+00  1.16086992092086E+00
> >  1.83754896486290E+01
> >   5.60009863356821E+00 -3.55360184993267E-01
> >  1.82504568294007E+01
> >   5.58914364795695E+00  8.10228710234038E+00
> >  1.51389875002830E+01
> >   1.15794247479560E+01  1.52694144559577E+00
> >  1.37711277243081E+01
> >   1.28383634052612E+01  5.11571607980042E+00
> >  2.01284534540082E+01
> >   1.69508684302737E+01 -1.04812430369407E+00
> >  2.11689116152223E+01
> >   1.77409434748636E+01  5.30549495482421E+00
> >  1.15541098433276E+01
> >  -1.12188435476261E+00  1.08626174281289E+01
> >  1.11423767086881E+01
> >   2.89157679340877E-01  1.87787040490874E+01
> >  1.61738341528294E+01
> >   4.98236213443105E+00  1.46260682731989E+01
> >  1.88044193480543E+01
> >   7.47991890414865E+00  1.63109639380093E+01
> >  1.22188263902333E+01
>
> === message truncated ===
>
>
> Mustafa Uludogan
> Chemical Engineering Department
> Texas A&M University
> College Station, TX 77843
>
>
>
> __________________________________
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-- 
Nuno Galamba
Grupo de Física-Matemática 
Complexo Interdisciplinar
Av. Prof Gama Pinto 2,  
1649-003 LISBOA   
PORTUGAL 

Voice: 21 790 48 59 Ext: 4259
email: ngalamba@cii.fc.ul.pt