[CP2K-user] [CP2K:13609] strange curve of the binding energy of Na-Cl

mejdeddine mokhtar mejdit... at gmail.com
Wed Jul 8 09:25:49 UTC 2020
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I appreciate your answer.
Unfornatullay, I used your values to plot the binding energy curve and I
didn't get the right curve as it should. The bong length is around 2.5
however the minimum energy is wrong, It should be -4.2 eV.
All the energies were referenced against the energy at a large distance (E
- Eref) where Eref=E[-1].
The x-axis was the distances and the y-axis was (E -Eref) / Hartree. I've
attached the plot.

Le mer. 8 juil. 2020 à 05:42, Lucas Lodeiro <eluni... at gmail.com> a
écrit :

> 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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