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[Anglade Pierre-Matthieu <anglade@gmail.com>]

Hi,

This is a quite different problem! 
from your post I can't tell either the energy stop being converged
after or before a particle get out of the box.  In the following I
will suppose that it is before; because otherwise this can be 1) either
a terrible bug 2) some "true coordinate" computation meaning that the
displayed coordinate is out of the box while there is an image particle
at the right place in the box and that this is not at all part of your
problem (my best guess).

So let's say that the problem is a convergence one.
It seems pretty natural as 
1)your box is wide,
2) it includes Na which is a metal,
3) I guess it's pretty much inhomogeneous after 150 step.

I know of only two tricks which may presently help a little bit in this case: 
1) playing with iscf (for instance use iscf 3 instead of 5)
2) playing with electronic temperature (tsmear)

Those two things may enable you to get a converged density

regards

PMA

On 9/26/05, Nuno Galamba <ngalamba@cii.fc.ul.pt> wrote:

Thanks for you answer Anglade

In fact the problem I have runned into in my MD simulations 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
  1.42863296997519E+01  9.66031303328476E+00  1.28482069102145E+01
  1.05373826482952E+01  1.75813280969912E+01  1.85699286439348E+01
  2.02139995948367E+01  1.42926205456365E+01   1.58161454757025E+01
  1.78909497953517E+01  1.99708303037689E+01  1.28418647876767E+01

vel
  3.61345755190633E-04  1.59222580487926E-04 -2.77175074102560E-05
-7.94124752426413E-04  2.62143756552861E-05   2.46005846575847E-04
  6.06414817868265E-05  4.86080442874640E-04 -5.69213988070817E-04
  1.94696258009353E-04  7.56388019803739E-05  1.55924145855197E-04
-6.81305347480819E-04 -6.88615541563244E-05  7.60960234425053E-04
  4.26915966036115E-04  1.66635414244097E-04 -2.32659334756115E-04
-1.99991078188162E-04  1.91948865478680E-04 -1.49301991428125E-04
  4.84155499711047E-05 -8.57300783824437E-05  2.18255753050848E-05
-3.03532143194674E-04 -1.43398741615671E-04  1.16603320920703E-05
-2.58727287730702E-04  2.17402859081001E-04  4.51481556108830E-04
-3.43055308460619E-04  1.90754552449349E-04  1.78812746828536E-04
-4.31953399259863E-04  3.62309251085063E-05 -4.55754759246047E-04
  6.40081806837475E-04  6.51547571151856E-04  1.00072373719001E-04
  5.44381826373121E-04 -2.70740536621591E-04 -1.91607989883120E-04
-2.48358368769158E-04 -8.74190122605132E-04 -1.52884001727244E-05
-3.60419313307425E-04  1.07639507430958E-03  1.61553411068105E-04
  2.13141742631626E-04  1.28701984080752E-05  2.58948971472996E-04
  2.57577902732932E-04  7.09749198743148E-04 -9.15557293102000E-05
  2.36831507122643E-04 -5.51371441063780E-04 -1.82064948476860E-04
-8.47405521228355E-06  5.49285683128093E-04 -3.81845184558150E-04
-4.11036573594706E-04 -2.12672547690139E-05  6.78055500494184E-04
-2.43250732701722E-04 -1.86492505154946E-04   3.87732680303958E-04
  4.59852228359158E-04 -2.28067503063192E-04  2.87374293466821E-04
  3.79436388130732E-04 -1.21622520562676E-04  4.28857628326593E-04
-5.66732944218849E-05  3.82666891466614E-05  3.55185691916205E-04
  1.62940953891326E-04  4.10183379721428E-04 -7.30677721712143E-04
-8.55537849604790E-05  2.48522310391418E-04 -6.39272002565119E-05
  6.91922912594730E-04  3.79786181579471E-04  2.85738195646260E-04
  3.48876992080368E-04   7.96703170255665E-05  5.82640845293898E-04
  7.03013539061508E-05  1.66492540632092E-04 -2.64740054178196E-04
-4.81057971763449E-04 -4.02538405413973E-04  5.91208606679974E-04
  6.84660363085143E-05 -6.31044301666006E-04   2.77728904985394E-04
-7.86667076780607E-05 -9.13710047240675E-05 -3.05484958554519E-04
-3.14497134487516E-04 -1.44788385895228E-04 -2.53397869895614E-04
  1.91776118159379E-04  6.20323794597650E-05  8.96482897085823E-06
-4.89657996883443E-04 -8.03974639952289E-05  1.44722036361834E-04
  3.19707866799983E-05 -2.70889502728457E-04  5.33791678975208E-05
-2.78349089043350E-06 -2.85186811447324E-04  1.61981842983486E-04
-1.04618748793896E-04 -2.28202988141319E-04  7.90379285890031E-06
-2.02693812792706E-04  8.69208240839734E-05 -1.84601881427213E-04
-8.50218656013146E-05 -8.39331545859563E-05  6.42536289917873E-04
  2.92505776294561E-04  3.63154915768707E-04   6.03155586847407E-05
-3.40104745704510E-05 -2.30454886952254E-04 -2.04088755425137E-04
-3.77072359684074E-04  3.97765835567884E-04  1.12993505119051E-04
  7.55670407586609E-05  9.70859721352099E-05  3.14167124563309E-04
-1.44434284361358E-04 -1.32708233980981E-04  5.47298003152002E-05
-6.08024450694477E-05 -4.97003786961105E-05 -3.11797153424798E-05
-8.56178777930613E-05  1.06254292787205E-04 -1.33999242621271E-04
-2.80479286292257E-05   9.74725746784787E-05 -4.75313418554370E-04
  2.44355000913113E-04 -8.43838982661567E-05 -1.07491644359097E-04
-4.81862237841437E-05  2.10948350585710E-04 -2.35769013621597E-05
  1.40524746720755E-04 -3.22263735677215E-04   2.88687187596357E-04
-4.11478798117340E-04 -2.69315384499740E-04 -2.36382259346532E-04
-1.07055033660231E-04 -9.75083786074954E-05  5.21628093244381E-05
  3.31081873016545E-04  2.04484191581289E-04 -2.88181851894121E-04
  3.42738488329567E-04 -7.15579211811260E-05  2.89191747320400E-04
-6.28194429251086E-05 -1.73710346766907E-04 -8.12427997233024E-04
  8.16713430019538E-05 -2.54381809707164E-04  2.91038657272049E-04
-1.55432610422003E-04   4.95419304109589E-06 -2.94084032674493E-05
  2.28510959359023E-04 -2.15854603544687E-04  2.24991198746045E-04
-4.41074379551528E-04  1.67034560302883E-04 -1.53824319378859E-04
  3.12748574781470E-04  2.67345432333349E-04 -1.77133432911651E-04
-3.24409756064884E-04 -4.25684700707660E-04 -1.97272277617721E-04
  3.78425379320122E-04  1.07138462246563E-05  2.29306378688200E-06

#Definition of the planewave basis set
ecut 35.0        # Maximal plane-wave kinetic energy cut-off, in Hartree

#Definition of the k-point grid

nkpt 1          # Only one k point is needed for isolated system,
                # taken by default to be 0.0 0.0 0.0

irdwfk 1        # Restart simulation with the wavefunction from a previous run

#Definition of the SCF procedure
iscf 5            #Control of the Self-Consistent Field method to be used
                  #The default is 5
nstep 50          # Maximal number of SCF cycles
toldfe 1.0d-6     # Will stop when, twice in a row, the difference
                  # between two consecutive evaluations of total energy
                  # differ by less than toldfe (in Hartree)
diemac 1.0        # Although this is not mandatory, it is worth to
                  # precondition the SCF cycle. The model dielectric
diemix 0.5        # function used as the standard preconditioner
                  # is described in the "dielng" input variable section.
                  # Here, we follow the prescriptions for molecules
                  # in a big box

# Molecular Dynamics Variables Setup
#
amu(2) 22.98977 35.453
ionmov 6                        # N,V,E MD using Verlet algorithm

dtion 206.71                     # time-step in atu 5fs

ntime 100


On Friday 23 September 2005 11:11, Anglade Pierre-Matthieu wrote:
> Hi,
>
> This won't answer your question but please consider the following:
> Molecular dynamics is chaotic and you'll never ever get exact results.
> Whatever precision you have for your computation you will always get
> results very differents (after even a not so big number of steps) from what
> a non arbitrary precision computation would gives.
> Then I would say that you can behaves in two different ways: either you
> choose to consider that molecular dynamics is not a suitable technic for
> your problem; or you decide not to mind that much about the differences
> resulting from a small error on your atoms phase space coordinates at the
> first restart step.
>
> regards
>
> PMA
>
> On 9/23/05, ngalamba@cii.fc.ul.pt <ngalamba@cii.fc.ul.pt> wrote:
> > Dear ABINIT users
> >
> > I am trying to use ABINIT to carry molecular dynamics simulations (N,V,E)
> > (IONMVOV 6) of simple ionic melts (e.g. NaCl).
> > Because it is hard to get a complete simulation on a single run without
> > computers crashing for some reason I have been trying to divide my
> > production runs in several stages that I therefore need to link.
> >
> > To link the partial simulations (say a 100 time-steps each with a
> > time-step of 5 fento seconds) I use the variable IRDWFK 1 to use the
> > wavefunction from the previous partial run and update the positions and
> > velocities in the new input file. ABINIT tells me that the file is good
> > for restarting the simulation and takes it from there.
> >
> > The "problem" is that the first time (MD step 1 not 0) ABINIT updates the
> > positions and velocities using the Verlet algorithm it only gives me the
> > first 6 digits of positions and velocities equal to those I would obtain
> > if I had continued the simulation on a single run. Then as more and more
> > integrations are performed the positions and velocities start to get more
> > and more different from those I would obtain in a single run.
> >
> > Is there any way of restarting a MD calculation in a such a way that the
> > results are identical whether we do it in several stages using the _WFK
> > files as input or in just a single run?
> >
> > I would be highly appreciated if anyone could give some hint on this type
> > of calculation as I am new to ABINIT and also to Hellman-Feynamnn MD.
> >
> > Thanks in advance.
> >
> > Nuno Galamba
>
> --
> Pierre-Matthieu Anglade

--
Nuno Galamba
Grupo de F�sica-Matem�tica
Complexo Interdisciplinar
Av. Prof Gama Pinto 2,
1649-003 LISBOA
PORTUGAL

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

-- 
Pierre-Matthieu Anglade