[CP2K-user] [CP2K:13607] strange curve of the binding energy of Na-Cl
Lucas Lodeiro
eluni... at gmail.com
Wed Jul 8 03:45:08 UTC 2020
Hello Mejdeddine,
for non-periodic calculations, you need to set "PERIODIC NONE" in &CELL
subsection too, to avoid pair interactions. Also, the cell need to be
grosser than the system density. I guess at large distances the system will
be Na⁺ and Cl⁻... for that the cell need to be, in the bond direction, the
bond distance + twice the ionic radii of the biggest ion to ensure the
density is zero at the borders, this is ~3.5 A due to the ionic radii of
Cl⁻ is 1.7 A.
Using WAVELET solver needs a cubic box, so, if you want to compute the
system at 10.0 A distance, the box will be 17.0A and cubic. With a cell of
10.0 A, you will have problems of non-zero density at 4.0 A distance, I
guess.
Otherwise, the EPSs values must be equal for SCF and OUT_SCF, and the
DEFAULT could be tightest (I use order of -6 and -12 respectively). And,
the number of inner cycles, is useful less steps to use the outer cycles
and improve the convergence.
Changing those things I get:
DIST (A) ENERGY(Ha)
1.0 -60.135198879741978
1.5 -61.855322129770521
2.0 -62.197077891951885
2.5 -62.227919856240661
3.0 -62.207241440696443
3.5 -62.182709877371700
4.0 -62.162755189608077
4.5 -62.148301846426023
5.0 -62.138459966222577
5.5 -62.131738730461414
6.0 -62.126565992226809
6.5 -62.122559283798338
7.0 -62.119778885873323
7.5 -62.118151081860589
8.0 -62.117267918233409
8.5 -62.116553100338109
9.0 -62.115268838231749
9.5 -62.114008578635961
10.0 -62.113128520139142
The minima is near 2.5 A, but I guess 2.6 A is closer... It is a coarse
grid for the potential profile.
Also, the sentence "tend to 1.5 eV even at a large distance.", according to
what I understand this value is arbitrary. At calculations this energy will
be the energy of isolated Cl⁻ plus isolated Na⁺... But is a pseudopotential
calculation, changing the pseudo or functional, the value will change. The
important value is the energy depth of the minima with respect to the large
converged distance. The large distance would be a coulomb r⁻¹ behavior.
I attach the input that I use to obtain list values.
Regards - Lucas Lodeiro
El mar., 7 jul. 2020 a las 10:21, mejdeddine mokhtar (<
mejdit... at gmail.com>) escribió:
> Thank's for your clarification.
> The curve should be showing a minimum of around 2.5 Angstrom and then tend
> to 1.5 eV even at a large distance. What I found is completely wrong, even
> after setting the &TOPOLOGY &CENTER COOR.
> I used the script below and the distance between both atoms is setting in
> the bash script. Any help would be appreciated.
> The curve should look like the one I've attached below.
>
>
> Le mar. 7 juil. 2020 à 14:31, Patrick Gono <patri... at gmail.com> a
> écrit :
>
>> Dear Mejdeddine,
>>
>> You are using a non-periodic Poisson solver, suitable for this system of
>> isolated atoms. However, the cell dimensions and atomic coordinates have to
>> be chosen in such a way that the electronic density on the edges of the
>> unit cell is negligible. Keep in mind that the cubic unit cell is situated
>> with one corner in location (0, 0, 0) and the opposite corner in (10, 10,
>> 10) Center the atoms in the middle of the cell, either manually, or by
>> switching on the CENTER_COORDINATES
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY/CENTER_COORDINATES.html> statement
>> in the TOPOLOGY
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html> section,
>> which should center them in the middle of the unit cell by default.
>>
>> Apart from that, I don't see any other immediate issue. What binding
>> energy plot do you get? What is strange about it?
>>
>> Yours sincerely,
>> Patrick Gono
>>
>> On Mon, 6 Jul 2020 at 14:56, mejdeddine mokhtar <mejdit... at gmail.com>
>> wrote:
>>
>>> Dear CP2K developers and users,
>>>
>>> I've tried to compute the binding energy of Na _ Cl (singlet state so
>>> the Multiplicity should be 1)but I got a strange curve at large distances.
>>> I don't have a lot o experience in using cp2k so I attached the script that
>>> I've used to calculate the potential energy at varying distance. Could
>>> someone check if I did something wrong? any help would be appreciated.
>>>
>>> &GLOBAL
>>> PROJECT NaCl
>>> RUN_TYPE ENERGY
>>> &END GLOBAL
>>>
>>> &FORCE_EVAL
>>>
>>> METHOD Quickstep
>>> &DFT
>>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>> CHARGE 0
>>> MULTIPLICITY 1
>>>
>>> &MGRID
>>> CUTOFF [Ry] 400
>>> &END
>>>
>>> &QS
>>> METHOD GPW
>>> EPS_DEFAULT 1.0E-6
>>> &END
>>>
>>> &POISSON # POISSON solver for non-periodic
>>> calculation
>>> PERIODIC NONE
>>> PSOLVER WAVELET
>>> &END
>>> &SCF
>>> SCF_GUESS ATOMIC ! can be used to RESTART an interrupted
>>> calculation
>>> MAX_SCF 300
>>> EPS_SCF 1.0E-6 ! accuracy of the SCF procedure typically 1.0E-6 -
>>> 1.0E-7
>>> &OT
>>> PRECONDITIONER FULL_SINGLE_INVERSE
>>> MINIMIZER DIIS
>>> &END OT
>>> &MIXING
>>> METHOD BROYDEN_MIXING
>>> ALPHA 0.4
>>> BETA 1.5
>>> NBROYDEN 8
>>> &END MIXING
>>> &OUTER_SCF ! repeat the inner SCF cycle 10 times
>>> MAX_SCF 100
>>> EPS_SCF 1.0E-5 ! must match the above
>>> OPTIMIZER DIIS
>>> &END
>>> &END SCF
>>> &XC
>>> &XC_FUNCTIONAL PBE
>>> &END XC_FUNCTIONAL
>>> &END XC
>>> &END DFT
>>> &SUBSYS
>>> &CELL
>>> ABC [angstrom] 10.00 10.00 10.00
>>> &END CELL
>>> &COORD
>>> Na 0.0 0.0 0.0
>>> Cl 0.0 0.0 MYDIST
>>> &END COORD
>>> &TOPOLOGY
>>> CONNECTIVITY GENERATE
>>> &GENERATE
>>> BONDLENGTH_MAX 9
>>> &END
>>> &END
>>> &KIND Na
>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &KIND Cl
>>> BASIS_SET DZVP-MOLOPT-SR-GTH
>>> POTENTIAL GTH-PBE
>>> &END KIND
>>> &END SUBSYS
>>> &END FORCE_EVAL
>>>
>>>
>>> The bash script used to get the calculation running is the following:
>>>
>>> rm -f ener_profile
>>>
>>> #for dist in `seq 2.3 0.1 6.0`
>>> for dist in 4.0 5.0 6.0 7.0 8.0 10.0; do
>>>
>>> #
>>> # compute energy
>>> #
>>> echo "Computing potential energy for distance $dist"
>>> sed "s/MYDIST/${dist}/g" mode1.inp > inp
>>> cp2k.popt inp > out
>>> ener=`grep ' ENERGY| Total FORCE_EVAL' out | awk '{print $NF}'`
>>> echo $dist $ener >> ener_profile
>>>
>>> done
>>>
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