[CP2K-user] [CP2K:19422] Re: super slow total dipole calculation for Mg2+ compared to Zn2+
Marcella Iannuzzi
marci.akira at gmail.com
Tue Oct 24 15:51:20 UTC 2023
Dear Emma,
If the MOS are localised the Wannier centers are also available and the
coordinates can be printed by activating the related print_key
- WANNIER_CENTERS
<https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/LOCALIZE/PRINT/WANNIER_CENTERS.html>
Regards
Marcella
On Tuesday, October 24, 2023 at 5:34:27 PM UTC+2 Emma Rossi wrote:
> Dear Marcella,
>
> Thank you very much for your reply.
>
> Actually, I’m using the Berry phase approach to compute the total dipole
> of the simulation box, thus I have not Wannier centres from my calculations
> at the moment.
>
> I tried several keywords for the minimisation of the wavefunction on
> single point calculations in gas phase. Conjugate Gradient in combination
> with the FULL_ALL preconditioner seems to speed up the calculation compared
> to DIIS and FULL_KINETIC preconditioner. I’ll try to use these
> settings for the MD in bulk.
>
> Using larger cutoffs for the electron density makes the calculations even
> slower.
>
> Concerning the band gap, I’ll check whether experimental data are
> available in the literature to assess the accuracy of my calculations.
>
> Thank you again for your hints.
>
> Best ragards,
> Emma Rossi
>
>
> Il giorno ven 20 ott 2023 alle 12:49 Marcella Iannuzzi <marci... at gmail.com>
> ha scritto:
>
>>
>>
>> Dear Emma,
>>
>> Both Mg and Na have quite hard functions in the basis set, it might be
>> that the cutoff of 600 Ry is not sufficient.
>> Have you checked whether the electronic structure is OK (e.g. energy
>> gap) ?
>> Often the localisation algorithm shows convergence problems when there
>> are intrinsically very delocalised states (see metals).
>> Maybe this is not the problem though. Are the Wannier centres after
>> localisation at the expected positions ?
>>
>> Regards
>> Marcella
>>
>>
>>
>> On Friday, October 20, 2023 at 11:09:48 AM UTC+2 Emma Rossi wrote:
>>
>>> Dear developers and CP2K users,
>>>
>>> I'm running AIMD simulations and computing the total dipole moment of a
>>> 15 A cubic box (Berry phase approach) containing water molecules, a
>>> phosphate chain (-4) and a divalent cation, either Zn2+ or Mg2+.
>>> For Mg2+, the convergence of the MOs localization process at each step
>>> is tremendously slower (one/two order of magnitude) compared to the box
>>> with Zn2+. I cannot figure out the reason of such behaviour. I use the
>>> default setting for the LOCALIZE section, which employs the JACOBI method.
>>>
>>> The -2 net charge of the system is counterbalanced by uniform
>>> background. 600 Ry cutoff for the auxiliary PW expansion of the electron
>>> density (500 or 400 Ry are used in the literature for Zn2+ and Mg2+
>>> respectively) and BLYP XC are used. DZVP-MOLOPT-SR-GTH-q10 and
>>> DZVP-MOLOPT-SR-GTH-q12 are used for Mg2+ and Zn2+ respectively.
>>>
>>> I observe a similar slowdown of the MOs localization speed when I use
>>> Na+ atoms to counterbalance the -2 charge of the system containing Zn2+.
>>>
>>> Here a typical input file follows.
>>>
>>> &GLOBAL
>>> PRINT_LEVEL LOW
>>> PROJECT_NAME MD
>>> RUN_TYPE MD
>>> &END GLOBAL
>>> &MOTION
>>> &MD
>>> ENSEMBLE NVT
>>> STEPS 100
>>> TIMESTEP 0.5
>>> TEMPERATURE 3.0000000000000000E+02
>>> TEMP_TOL 5.0000000000000000E+01
>>> &THERMOSTAT
>>> TYPE CSVR
>>> &CSVR
>>> TIMECON 2.4999999999999996E+01
>>> &END CSVR
>>> &END THERMOSTAT
>>> &END MD
>>> &END MOTION
>>> &FORCE_EVAL
>>> METHOD QS
>>> &DFT
>>> BASIS_SET_FILE_NAME BASIS_MOLOPT
>>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>>> CHARGE -2
>>> &SCF
>>> MAX_SCF 100
>>> EPS_SCF 4.9999999999999998E-07
>>> SCF_GUESS RESTART
>>> &OT T
>>> MINIMIZER DIIS
>>> PRECONDITIONER FULL_KINETIC
>>> &END OT
>>> &END SCF
>>> &MGRID
>>> CUTOFF 6.0000000000000000E+02
>>> &END MGRID
>>> &XC
>>> DENSITY_CUTOFF 1.0000000000000000E-10
>>> GRADIENT_CUTOFF 1.0000000000000000E-10
>>> TAU_CUTOFF 1.0000000000000000E-10
>>> &XC_GRID
>>> XC_SMOOTH_RHO NN10
>>> XC_DERIV SPLINE2_SMOOTH
>>> &END XC_GRID
>>> &XC_FUNCTIONAL NO_SHORTCUT
>>> &BECKE88 T
>>> &END BECKE88
>>> &LYP T
>>> &END LYP
>>> &END XC_FUNCTIONAL
>>> &VDW_POTENTIAL
>>> &PAIR_POTENTIAL
>>> R_CUTOFF 8.0000000000000000E+00
>>> TYPE DFTD3(BJ)
>>> PARAMETER_FILE_NAME dftd3.dat
>>> REFERENCE_FUNCTIONAL BLYP
>>> EPS_CN 1.0000000000000000E-02
>>> CALCULATE_C9_TERM T
>>> REFERENCE_C9_TERM T
>>> LONG_RANGE_CORRECTION T
>>> &END PAIR_POTENTIAL
>>> &END VDW_POTENTIAL
>>> &END XC
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> * &LOCALIZE T &PRINT &TOTAL_DIPOLE ON
>>> FILENAME =totdipole PERIODIC T &EACH MD
>>> 1 &END EACH &END TOTAL_DIPOLE &END PRINT &END
>>> LOCALIZE*
>>> &END DFT
>>> &SUBSYS
>>> &CELL
>>> A 1.5460000000000001E+01 0.0000000000000000E+00
>>> 0.0000000000000000E+00
>>> B 0.0000000000000000E+00 1.5460000000000001E+01
>>> 0.0000000000000000E+00
>>> C 0.0000000000000000E+00 0.0000000000000000E+00
>>> 1.5460000000000001E+01
>>> MULTIPLE_UNIT_CELL 1 1 1
>>> &END CELL
>>> &KIND O
>>> BASIS_SET DZVP-MOLOPT-GTH-q6
>>> POTENTIAL GTH-BLYP-q6
>>> &END KIND
>>> &KIND H
>>> BASIS_SET DZVP-MOLOPT-GTH-q1
>>> POTENTIAL GTH-BLYP-q1
>>> &END KIND
>>> &KIND C
>>> BASIS_SET DZVP-MOLOPT-GTH-q4
>>> POTENTIAL GTH-BLYP-q4
>>> &END KIND
>>> &KIND P
>>> BASIS_SET DZVP-MOLOPT-GTH-q5
>>> POTENTIAL GTH-BLYP-q5
>>> &END KIND
>>> &KIND Na
>>> BASIS_SET DZVP-MOLOPT-SR-GTH-q9
>>> POTENTIAL GTH-BLYP-q9
>>> &END KIND
>>> &KIND Mg
>>> BASIS_SET DZVP-MOLOPT-SR-GTH-q10
>>> POTENTIAL GTH-BLYP-q10
>>> &END KIND
>>> &TOPOLOGY
>>> NUMBER_OF_ATOMS 384
>>> MULTIPLE_UNIT_CELL 1 1 1
>>> &END TOPOLOGY
>>> &END SUBSYS
>>> &END FORCE_EVAL
>>>
>>> Here a piece of the *file.out* concerning the *localization* is reported
>>>
>>> ENSEMBLE TYPE =
>>> NVT
>>> STEP NUMBER =
>>> 48740
>>> TIME [fs] =
>>> 24370.000000
>>> CONSERVED QUANTITY [hartree] =
>>> -0.234908827385E+04
>>>
>>> INSTANTANEOUS
>>> AVERAGES
>>> CPU TIME [s] = 220.24
>>> 29.11
>>> ENERGY DRIFT PER ATOM [K] = -0.274167730955E+04
>>> -0.106732023761E+04
>>> POTENTIAL ENERGY[hartree] = -0.235022491736E+04
>>> -0.234811418791E+04
>>> KINETIC ENERGY [hartree] = 0.530388799833E+00
>>> 0.547854613121E+00
>>> TEMPERATURE [K] = 291.529
>>> 301.129
>>> ***************************
>>>
>>>
>>> Number of electrons:
>>> 1070
>>> Number of occupied orbitals:
>>> 535
>>> Number of molecular orbitals:
>>> 535
>>>
>>> Number of orbital functions:
>>> 3012
>>> Number of independent orbital functions:
>>> 3012
>>>
>>> Extrapolation method: ASPC
>>>
>>> SCF WAVEFUNCTION OPTIMIZATION
>>>
>>> ----------------------------------- OT
>>> ---------------------------------------
>>> Minimizer : DIIS : direct inversion
>>> in the iterative subspace
>>> using 7 DIIS vectors
>>> safer DIIS on
>>> Preconditioner : FULL_KINETIC : inversion of T + eS
>>> Precond_solver : DEFAULT
>>> stepsize : 0.15000000 energy_gap :
>>> 0.20000000
>>> eps_taylor : 0.10000E-15 max_taylor :
>>> 4
>>> ----------------------------------- OT
>>> ---------------------------------------
>>>
>>> Step Update method Time Convergence Total energy
>>> Change
>>>
>>> ------------------------------------------------------------------------------
>>> 1 OT DIIS 0.15E+00 4.9 0.00001365 -2350.2265786077
>>> -2.35E+03
>>> 2 OT DIIS 0.15E+00 7.0 0.00000785 -2350.2266129356
>>> -3.43E-05
>>> 3 OT DIIS 0.15E+00 7.0 0.00000667 -2350.2266281036
>>> -1.52E-05
>>> 4 OT DIIS 0.15E+00 7.0 0.00000316 -2350.2266318502
>>> -3.75E-06
>>> 5 OT DIIS 0.15E+00 7.1 0.00000285 -2350.2266340790
>>> -2.23E-06
>>> 6 OT DIIS 0.15E+00 7.0 0.00000168 -2350.2266355491
>>> -1.47E-06
>>> 7 OT DIIS 0.15E+00 7.1 0.00000158 -2350.2266365271
>>> -9.78E-07
>>> 8 OT DIIS 0.15E+00 7.0 0.00000079 -2350.2266370647
>>> -5.38E-07
>>> 9 OT DIIS 0.15E+00 7.1 0.00000054 -2350.2266374235
>>> -3.59E-07
>>> 10 OT DIIS 0.15E+00 7.0 0.00000041 -2350.2266374897
>>> -6.63E-08
>>>
>>> * SCF run converged in 10 steps *
>>>
>>>
>>> Electronic density on regular grids: -1069.9999984366
>>> 0.0000015634
>>> Core density on regular grids: 1067.9999999649
>>> -0.0000000351
>>> Total charge density on r-space grids: -1.9999984716
>>> Total charge density g-space grids: -1.9999984716
>>>
>>> Overlap energy of the core charge distribution:
>>> 0.00000352123302
>>> Self energy of the core charge distribution:
>>> -6058.29367128599642
>>> Core Hamiltonian energy:
>>> 1758.83041225385932
>>> Hartree energy:
>>> 2514.80853697306702
>>> Exchange-correlation energy:
>>> -565.57191895188691
>>>
>>> Total energy:
>>> -2350.22663748972354
>>>
>>> LOCALIZE| The spread relative to a set of orbitals is computed
>>> LOCALIZE| Orbitals to be localized: All orbitals
>>> LOCALIZE| If fractional occupation, fully occupied MOs are those
>>> within occupation tolerance of 0.00000001
>>> LOCALIZE| Spread defined by the Berry phase operator
>>> LOCALIZE| Optimal unitary transformation generated by Jacobi algorithm
>>>
>>> Eigenvalues of the occupied subspace spin 1
>>> ---------------------------------------------
>>> -2.77340522 -1.55519360 -1.55401616 -1.55312686
>>> -0.84401306 -0.81554322 -0.80702571 -0.80237237
>>> -0.80085752 -0.79902548 -0.79112340 -0.79067760
>>> -0.78889214 -0.78844561 -0.78745096 -0.78661985
>>> -0.78594483 -0.78398619 -0.78359896 -0.78223867
>>> -0.78202387 -0.78089859 -0.77900446 -0.77831838
>>> -0.77761721 -0.77700210 -0.77677871 -0.77654095
>>> -0.77610461 -0.77529141 -0.77482833 -0.77403370
>>> [.......]
>>> -0.09177880 -0.09168157 -0.09118981 -0.09045276
>>> -0.09027640 -0.08911508 -0.08871380 -0.08817562
>>> -0.08660485 -0.08624312 -0.08399649 -0.08220911
>>> -0.07894380 -0.07429071 -0.06779908
>>> Fermi Energy [eV] : -1.844907
>>>
>>> LOCALIZATION| Computing localization properties for OCCUPIED ORBITALS.
>>> Spin: 1
>>> Spread Functional sum_in -w_i ln(|z_in|^2) sum_in
>>> w_i(1-|z_in|^2)
>>> Initial Spread (Berry) : 203183.2008851338 34522.
>>> 9346453651 <(934)%20645-3651>
>>> Localization by iterative distributed Jacobi rotation
>>> Iteration Functional Tolerance
>>> Time
>>> 100 1035.1444747551 0.7611E-01
>>> 0.145
>>> 200 1035.1439265702 0.2374E-01
>>> 0.145
>>> 300 1035.1438285431 0.2086E-01
>>> 0.145
>>> 400 1035.1437772042 0.1457E-01
>>> 0.155
>>> 500 1035.1437553092 0.8452E-02
>>> 0.146
>>> 600 1035.1437479886 0.4565E-02
>>> 0.156
>>> 700 1035.1437457665 0.2413E-02
>>> 0.144
>>> 800 1035.1437451192 0.1268E-02
>>> 0.155
>>> 900 1035.1437449348 0.6661E-03
>>> 0.155
>>> 1000 1035.1437448830 0.3497E-03
>>> 0.156
>>> 1100 1035.1437448685 0.1836E-03
>>> 0.169
>>> Localization for spin 1 converged in 1195 iterations
>>> Spread Functional sum_in -w_i ln(|z_in|^2) sum_in
>>> w_i(1-|z_in|^2)
>>> Total Spread (Berry) : 1051.8315283360
>>> <(831)%20528-3360> 1035.1437448646
>>>
>>> To check the role of the localization method in such problem, I ran two
>>> single point calculations, the first using the JACOBI method and the second
>>> using the CRAZY method to compute the total dipole. The latter makes the
>>> process even slower.
>>>
>>> I would be very grateful if any of you could give me any insight.
>>>
>>> Best regards,
>>> Emma Rossi
>>
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