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

Travis polla... at gmail.com
Wed Jul 8 11:05:42 UTC 2020
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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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>>>>> <https://groups.google.com/d/msgid/cp2k/0798c015-5b94-4175-9179-71f3c2a5b5e3o%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
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>>>> <https://groups.google.com/d/msgid/cp2k/CAPL1_v95qaJijWmSD31i3%2B3RLU-QrDakeNe12fgb0DG6ELi%2BpQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>> .
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>>> <https://groups.google.com/d/msgid/cp2k/CAHBAvwt1JXXfps0wB3CxPi7PpZxOcPn5BDbwjhrM204H8eoP5A%40mail.gmail.com?utm_medium=email&utm_source=footer>
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> To view this discussion on the web visit 
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>> <https://groups.google.com/d/msgid/cp2k/CAOFT4PKcbV-0HiTsT7fo%3DU3WYbWm1YX4dUgiuqh33NLo3NZwgQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
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>
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