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[ngalamba@cii.fc.ul.pt]

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
  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 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