I am sorry, I am a freshman about the siesta. The input is listed in the
following.
My calculations about the binding energy do not meet the experimental
results,so,I have to check the ghost atoms calculations.Now,The impact is
acceptable.
Another problem is how to get the chemical potential or total energy of
free C or N atom. Does it need to calculate the the ghost atoms affected by the
supercell?
SystemName C62N_ghost
SystemLabel C62N_ghost
NumberOfSpecies 3
%block ChemicalSpeciesLabel
1 6 C
2 7 N
3 -6 Cg
%endblock ChemicalSpeciesLabel
%block PS.lmax
C 1
%endblock PS.lmax
%include coord.fdf
PAO.BasisSize DZP
#SolutionMethod dm_on
SolutionMethod diagon
MeshCutoff 200.0000000 Ry
#MD.TypeOfRun Broyden
#MD.TypeOfRun CG
#MD.NumCGsteps 500
WriteForces
MD.MaxForceTol 0.04 eV/Ang
#DM.UseSaveDM T
MaxSCFIterations 100
DM.MixingWeight 0.1
DM.NumberPulay 6
#DM.MixingWeight 0.25
#DM.NumberPulay 0
SpinPolarized .true.
#FixSpin .true.
#TotalSpin 2.0
WriteMullikenPop 1
NetCharge -1.0
%block kgrid_Monkhorst_Pack
2 0 0 0.0
0 2 0 0.0
0 0 2 0.0
%endblock kgrid_Monkhorst_Pack
> -----Original E-mail-----
> From: "Herbert Fruchtl" <herbert.fruc...@st-andrews.ac.uk>
> Sent Time: 2011-3-18 20:06:46
> To: siesta-l@uam.es
> Cc:
> Subject: Re: [SIESTA-L] about basis-set superposition error (BSSE)
>
> From the energy part of the output alone we can't tell if the input was
> correct. You see a smallish difference and lower energy with the ghost, which
> one would expect.
>
> Total energies are meaningless, and of course adding a few basis functions
> won't
> change the total by a lot. You need to compare differences (like a binding
> energy, as you indicated in your original post).
>
> In the example outputs below, the difference (in absolute energies) is 0.09
> eV.
> That's 2 kcal/mol or 9 kJ/mol. Depending on the interaction you are looking
> at,
> this may or may not be negligible.
>
> Herbert
>
> On 03/18/2011 02:00 AM, Wei Hu wrote:
> > Dear,the ghost atoms calculations seem to little effects on the total
> > energy from my results. Is there any wrong?
> >
> > My results about a nitrogen-vacancy center in bulk diamond C62N (2*2*2):
> >
> > The results with ghost atoms:
> >
> > siesta: Program's energy decomposition (eV):
> > siesta: Eions = 16680.576136
> > siesta: Ena = 3653.202863
> > siesta: Ekin = 7163.588024
> > siesta: Enl = -820.400928
> > siesta: DEna = -182.458272
> > siesta: DUscf = 15.575306
> > siesta: DUext = 0.000000
> > siesta: Exc = -3054.613637
> > siesta: eta*DQ = 0.000000
> > siesta: Emadel = 0.000000
> > siesta: Ekinion = 0.000000
> > siesta: Eharris = -9905.679557
> > siesta: Etot = -9905.682781
> > siesta: FreeEng = -9905.682783
> >
> > siesta: Final energy (eV):
> > siesta: Kinetic = 7163.588024
> > siesta: Hartree = 894.608032
> > siesta: Ext. field = 0.000000
> > siesta: Exch.-corr. = -3054.613637
> > siesta: Ion-electron = -8393.758885
> > siesta: Ion-ion = -6515.506314
> > siesta: Ekinion = 0.000000
> > siesta: Total = -9905.682781
> >
> > The results without ghost atoms:
> >
> > siesta: Program's energy decomposition (eV):
> > siesta: Eions = 16680.576136
> > siesta: Ena = 3653.202863
> > siesta: Ekin = 7164.385562
> > siesta: Enl = -820.554764
> > siesta: DEna = -182.943454
> > siesta: DUscf = 15.589130
> > siesta: DUext = 0.000000
> > siesta: Exc = -3054.694636
> > siesta: eta*DQ = 0.000000
> > siesta: Emadel = 0.000000
> > siesta: Ekinion = 0.000000
> > siesta: Eharris = -9905.587400
> > siesta: Etot = -9905.591435
> > siesta: FreeEng = -9905.591437
> >
> > siesta: Final energy (eV):
> > siesta: Kinetic = 7164.385562
> > siesta: Hartree = 894.861106
> > siesta: Ext. field = 0.000000
> > siesta: Exch.-corr. = -3054.694636
> > siesta: Ion-electron = -8394.637153
> > siesta: Ion-ion = -6515.506314
> > siesta: Ekinion = 0.000000
> > siesta: Total = -9905.591435
> >
> >
> >
> >
> >> -----Original E-mail-----
> >> From: "Herbert Fruchtl"<herbert.fruc...@st-andrews.ac.uk>
> >> Sent Time: 2011-3-17 22:36:53
> >> To: siesta-l@uam.es
> >> Cc:
> >> Subject: Re: [SIESTA-L] about basis-set superposition error (BSSE)
> >>
> >> You can calculate counterpoise-corrected energies by specifying ghost
> >> atoms.
> >> There is no way of doing counterpoise-corrected geometry optimisations in
> >> SIESTA.
> >>
> >> Herbert
> >>
> >> On 03/17/2011 01:57 PM, yf liu wrote:
> >>> Hello everybody,
> >>>
> >>> whether the basis-set superposition error (BSSE) is included in siesta
> >>> calculation. when i calculate the molecule adsorption on carbon nanotube,
> >>> i
> >>> found the adsorption energy is some higher than the well know value. how
> >>> can i
> >>> add the BSSE in siesta calculation?
> >>>
> >>> yours
> >>> yufeng liu
> >>>
> >>
> >> --
> >> Herbert Fruchtl
> >> Senior Scientific Computing Officer
> >> School of Chemistry, School of Mathematics and Statistics
> >> University of St Andrews
> >> --
> >> The University of St Andrews is a charity registered in Scotland:
> >> No SC013532
> >
>
> --
> Herbert Fruchtl
> Senior Scientific Computing Officer
> School of Chemistry, School of Mathematics and Statistics
> University of St Andrews
> --
> The University of St Andrews is a charity registered in Scotland:
> No SC013532
