[CP2K-user] [CP2K:19470] Re: super slow total dipole calculation for Mg2+ compared to Zn2+
Emma Rossi
emma.rossi.1 at studenti.unipd.it
Mon Nov 6 10:00:10 UTC 2023
Dear Dr. Krack,
thank you for your reply.
I tested different cutoffs ranging from 1200 to 2200 Ry, but I cannot
observe any improvement in the speed of the MOs localization procedure.
I tried also GAPW with 1200 Ry instead of GPW, which is the default, since
I've read that it had been suggested on this google group for a similar
problem with Na+.
It seems that the problem does not depend on the details of the electronic
structure settings for Mg2+.
I attached some graphs of the iterations needed to converge the dipole in
the different tests I did. Hope this might help.
1)TEST 1 : Mg2+ DIIS, 1200 RY, JACOBI vs Zn2+ DIIS, 600 Ry, JACOBI
2)TEST 2: Mg2+ DIIS, JACOBI, 1200-2200 Ry (fixed maximum computing time)
3) TEST 3: Mg2+ DIIS, JACOBI, 1200 Ry GPW vs.GAPW. (fixed maximum computing
time)
Thank you again for your availability in discussing.
Best regards,
Emma Rossi
Il giorno gio 2 nov 2023 alle ore 16:29 Krack Matthias <
matthias.krack at psi.ch> ha scritto:
> Dear Emma
>
>
>
> The electronic structure of Mg(2+) (2s2 2p6) and Zn(2+) (3d10) is anything
> than similar. The very great hardness of the Mg-q10 pseudopotential, as
> already noted by Marcella, has been discussed several times on this forum.
> It requires with GPW cutoff values of 1200 Ry or larger for converged
> forces.
>
>
>
> HTH
>
>
>
> Matthias
>
>
>
> *From: *cp2k at googlegroups.com <cp2k at googlegroups.com> on behalf of Emma
> Rossi <emma.rossi.1 at studenti.unipd.it>
> *Date: *Thursday, 2 November 2023 at 15:55
> *To: *cp2k at googlegroups.com <cp2k at googlegroups.com>
> *Subject: *Re: [CP2K:19451] Re: super slow total dipole calculation for
> Mg2+ compared to Zn2+
>
> 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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