[CP2K-user] [CP2K:13612] strange curve of the binding energy of Na-Cl

Lucas Lodeiro eluni... at gmail.com
Wed Jul 8 21:43:49 UTC 2020
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The energy at 10.0 A is not a well behaved as "real large distance"...
remember the ion interact throw coulomb interaction, charges of +1 and -1
have a interaction energy at 10.0 A of 1.4 eV, if we use this crude
approximation, the energy of the minima is -4.5 eV respect to "converged
large distance". Also you can calculate the isolated Na⁺ and Cl⁻, to get
the infinite distance reference.
But if you want numeric accuracy, you need to use a better basis set at
least, with diffuse and TZ, and maybe another functional.

El mié., 8 jul. 2020 a las 8:22, mejdeddine mokhtar (<mejdit... at gmail.com>)
escribió:

> Hi Travis,
> I meant that it should be -4.2 or -4.3, I found from another code (GPAW)
> the right curve but using cp2k I'm unable to get it. I think some
> parameters should be set correctly.
>
> Best.
>
> Mejdeddine
>
> Le mer. 8 juil. 2020 à 13:05, Travis <polla... at gmail.com> a écrit :
>
>> Hi,
>>
>> I think you've converted incorrectly. Minimum at 2.5 Angstroms is -3.12
>> eV based on the data above.
>>
>> -T
>>
>> On Wednesday, July 8, 2020 at 5:26:06 AM UTC-4 mej... at gmail.com wrote:
>>
>>> 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 <el... 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 (<
>>>> mej... 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 <pat... 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 <mej... 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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>>>>>>>
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