[CP2K-user] [CP2K:19451] Re: super slow total dipole calculation for Mg2+ compared to Zn2+
Emma Rossi
emma.rossi.1 at studenti.unipd.it
Thu Nov 2 14:54:02 UTC 2023
Dear Marcella,
I checked the Wannier centers of the system and they are properly localized.
I tried running the dynamics also with 800 Ry cutoff (vs. 600 Ry used
previously), CG minimization algorithm for the wfn (vs. DIIS ) and CRAZY
method (vs. JACOBI) for the calculation of the dipole moment. These
settings do not improve the situation.
I cannot figure out the reason why the localization of the total dipole
moment for Mg2+ requires many more iterations per step compared to Zn2+.
These metals have very similar electronic structure, 10 and 12 valence
electrons respectively, and using the same level of theory, the calculation
for the two takes very different time scales.
I'm going to compute both the band gap and the Wannier centers also for the
system with Zn2+, just to compare.
Thank you for your suggestions and any further discussions are highly
appreciated.
Best regards,
Emma Rossi
Il giorno mar 24 ott 2023 alle ore 17:51 Marcella Iannuzzi <
marci.akira at gmail.com> ha scritto:
>
>
> 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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