Dear Herbert Fruchtl:
thank you very much for your reply. I have read the manual carefully,
but find little message about the ghost atoms. the new question is: How can
I use the ghost atom to correct the binding energy etc. ? For example, I
want correct the calculation about the molecule adsorption on the nanotube.
Should I set a ghost atom between the molecule and the nanotube ?
looking forward your reply.
2011/3/20 Wei Hu <gyrw4...@mail.ustc.edu.cn>
> 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
>
>
