[CP2K-user] [CP2K:19400] super slow total dipole calculation for Mg2+ compared to Zn2+
Emma Rossi
emma.rossi.1 at studenti.unipd.it
Fri Oct 20 09:09:48 UTC 2023
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
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
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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