[Pw_forum] Bonding Energy

[FELIPE VALENCIA]

Dear MIchael,

> Dear PWscf users,
> 
> I have tried to calculate bonding energy between Ni-Ni and Pd-Pd. Then I
> would try to calculate energy of a layer.
> The file to calculate Ni-Ni I have used from example1 file and modify it to
> my case, but I got "strange" results (to both calculations).

Well, the files from example1 are intended for crystall calculations, so
if you are modeling molecular systems, you must change a few things.

First, as stated by Eyvaz, you should better use a simple cubic lattice
(ibrav=1) or even better a free lattice (ibrav=0, and take a look to
example3)

Next, remember that atomic coordinatives are  written scaled
to the lattice parameter ( celldm(1) ), and that the lattice parameter is
written in atomic units.

As pwscf  makes use of plane wave expantions, whenever you calculate a
molecule, you are also considering its "images" wich have a peridicity
given by alat (celldm(1)), In order to minimize the ghost interacitions,
you should increase alat until the results are no longer dependent on it.
That is why it is better to use the free lattice: you can choose
celldm(1) = 1.0, so that  the atomic coordinates are written in atomic
units, and  then change  the lattice vectores (again see example3) until
the
image interactions get negligible.

Hope it will be usefull,
Felipe
> Therefore I have two questions involving my calculations:
> 1. Can PWscf make so type of calculations? If so can You tell my what am I
> doing wrong?
> 2. How can I calculate celldm(1) in general (for example for Pd), I know the
> cell parameters but I
> don't know how to translate them to celldm(1).
> I think it should be exact value (or could it be estimated?).
> 
> Please forgive me if those are trivial questions, but I am new in this field
> and I am learning ( I am undergraduate student).
> I also want to ask if You could recommend  me some articles or ("good") web
> pages about Ni, Pd (e.g. experimental values) k-points and
> things which You think I should read to understand more about program and my
> problem (catalysis).
> 
> I enclose example files for Ni.
> 
> Thanks,
>                 Michal
> 
> #
> # self-consistent calculation
> #
> cat > ni.scf0.in << EOF
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
>     prefix='ni'
>     tprnfor = .true.,
>     tstress = .true.
>  /
>  &system
>     ibrav=2, celldm(1) =6.48, nat=1, ntyp=1,
>     nspin = 2,  starting_magnetization(1)=0.7,
>     ecutwfc = 24.0, ecutrho = 288.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>  /
>  &electrons
>     conv_thr = 1.0e-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Ni 58.69 NiUS.RRKJ3.UPF
> ATOMIC_POSITIONS{angstrom}
>  Ni 0.0 0.0 0.0
> K_POINTS{gamma}
> EOF
> 
> #
> # self-consistent calculation
> #
> for i in `seq 1.0 0.1 5.0`;do
> cat > ni.scf$i.in << EOF
>  &control
>     calculation='scf'
>     restart_mode='from_scratch',
>     pseudo_dir = '$PSEUDO_DIR/',
>     outdir='$TMP_DIR/'
>     prefix='ni'
>     tprnfor = .true.,
>     tstress = .true.
>  /
>  &system
>     ibrav=2, celldm(1) =6.48, nat=2, ntyp=1,
>     nspin = 2,  starting_magnetization(1)=0.7,
>     ecutwfc = 24.0, ecutrho = 288.0,
>     occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>  /
>  &electrons
>     conv_thr = 1.0e-8
>     mixing_beta = 0.7
>  /
> ATOMIC_SPECIES
>  Ni 58.69 NiUS.RRKJ3.UPF
> ATOMIC_POSITIONS{angstrom}
>  Ni 0.0 0.0 0.0
>  Ni $i  0.0 0.0
> K_POINTS{gamma}
> EOF
> 
> 
> 
> 
> 
> 
> 
> 
> 
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