optimization of Au(111) with organic adsorbant does not converged with OT scheme
170 views
Skip to first unread message
DMITRII Drugov
Mar 7, 2021, 7:34:38 PM3/7/21
to cp2k
Hi guys, could you please explain why my Au(111) + molecule on top does not converged with OT scheme. I try to use diagonalization before with smearing at 300 K and 1000 K electronic temperature but it didn't give me reasonable results in Ead energy despite system converged. Graphite system works well with this settings.
Regrads,
Dmitrii
&GLOBAL
PROJECT Au111_optimisation_larger_cell_plus_cluster1
RUN_TYPE GEO_OPT
PRINT_LEVEL MEDIUM
!EXTENDED_FFT_LENGTHS
&END GLOBAL
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
CHARGE -1
MULTIPLICITY 1
&MGRID
CUTOFF 800
NGRIDS 5
REL_CUTOFF 70
&END MGRID
&QS
EPS_DEFAULT 1.0E-14
!WF_INTERPOLATION ASPC
&END QS
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-7
MAX_SCF 40
&OT
MINIMIZER DIIS
PRECONDITIONER FULL_KINETIC
# ENERGY_GAP 0.01
&END OT
&OUTER_SCF
EPS_SCF 1E-6
MAX_SCF 20
&END
!CHOLESKY INVERSE
!ADDED_MOS 100
!&SMEAR ON
! METHOD FERMI_DIRAC
! ELECTRONIC_TEMPERATURE [K] 1000
! &END SMEAR
!&DIAGONALIZATION
! ALGORITHM STANDARD
!&END DIAGONALIZATION
!&MIXING
! METHOD BROYDEN_MIXING
!ALPHA 0.4
!NBROYDEN 8
!&END MIXING
&END SCF
&XC
&XC_FUNCTIONAL
&PBE
&END PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF 15.0
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&POISSON
PERIODIC xy
POISSON_SOLVER ANALYTIC
&END POISSON
&END DFT
&SUBSYS
&CELL
ABC 19.97928 17.30256 50.0
ALPHA_BETA_GAMMA 90.0 90.0 90.0
PERIODIC xy
&END CELL
&COORD
Au 0.2557400000 -0.0075500000 -0.2940100000
Au 0.7647600000 1.4555400000 4.7804700000
Au 3.2592100000 -0.0186000000 4.7812500000
Au 1.7334400000 -0.0062200000 2.2808300000
Au 4.2300800000 1.4624200000 2.2817200000
Au 2.7526900000 1.4436200000 -0.2881100000
Au -0.2569100000 -0.0074500000 7.3598400000
Au 2.2400900000 1.4440500000 7.3505400000
Au 0.2562800000 2.8739900000 -0.2980800000
Au 0.7665000000 4.3361400000 4.7777900000
Au 3.2619600000 2.8671500000 4.7803000000
Au 1.7321400000 2.8791700000 2.2824400000
Au 4.2318700000 4.3460600000 2.2819600000
Au 2.7520400000 4.3293500000 -0.2918800000
Au -0.2573700000 2.8754800000 7.3635900000
Au 2.2380300000 4.3288400000 7.3503900000
Au 0.2557200000 5.7621400000 -0.2922500000
Au 0.7672800000 7.2195900000 4.7801200000
Au 3.2609900000 5.7548900000 4.7837600000
Au 1.7339800000 5.7564700000 2.2835300000
Au 4.2298300000 7.2260200000 2.2856000000
Au 2.7529900000 7.2152500000 -0.2964400000
Au -0.2572400000 5.7624900000 7.3556900000
Au 2.2382200000 7.2136300000 7.3605500000
Au 0.2560900000 8.6521800000 -0.2869400000
Au 0.7650700000 10.1054800000 4.7812800000
Au 3.2595500000 8.6387800000 4.7854800000
Au 1.7333300000 8.6322600000 2.2867400000
Au 4.2269400000 10.1071700000 2.2830700000
Au 2.7541600000 10.0982200000 -0.2920900000
Au -0.2550200000 8.6517600000 7.3522000000
Au 2.2419200000 10.0985300000 7.3597400000
Au 0.2572000000 11.5362000000 -0.2929100000
Au 0.7623300000 12.9923400000 4.7810700000
Au 3.2591900000 11.5202300000 4.7788300000
Au 1.7321300000 11.5157200000 2.2843200000
Au 4.2271300000 12.9915200000 2.2780400000
Au 2.7546500000 12.9804800000 -0.2912300000
Au -0.2531600000 11.5355900000 7.3537100000
Au 2.2441500000 12.9807100000 7.3548500000
Au 0.2563800000 14.4161100000 -0.2940400000
Au 0.7626400000 15.8772300000 4.7825500000
Au 3.2576200000 14.4018000000 4.7784000000
Au 1.7341800000 14.4055200000 2.2796600000
Au 4.2281900000 15.8778400000 2.2800300000
Au 2.7535900000 15.8628800000 -0.2917000000
Au -0.2545500000 14.4146300000 7.3539700000
Au 2.2423000000 15.8625600000 7.3555700000
Au 5.2504700000 -0.0031500000 -0.2873300000
Au 5.7554300000 1.4496900000 4.7827800000
Au 8.2564200000 -0.0223400000 4.7844200000
Au 6.7305500000 -0.0153600000 2.2838600000
Au 9.2272600000 1.4536000000 2.2838000000
Au 7.7494800000 1.4492800000 -0.2949300000
Au 4.7366500000 -0.0017500000 7.3605200000
Au 7.2346300000 1.4505900000 7.3558500000
Au 5.2497200000 2.8792300000 -0.2914800000
Au 5.7558000000 4.3399700000 4.7814900000
Au 8.2540900000 2.8610600000 4.7825900000
Au 6.7324600000 2.8674200000 2.2839900000
Au 9.2298600000 4.3401400000 2.2819300000
Au 7.7491300000 4.3295300000 -0.2929000000
Au 4.7360700000 2.8818600000 7.3608600000
Au 7.2349000000 4.3300800000 7.3539700000
Au 5.2492200000 5.7623700000 -0.2921900000
Au 5.7584400000 7.2324100000 4.7809700000
Au 8.2522300000 5.7492600000 4.7846100000
Au 6.7327700000 5.7486600000 2.2831600000
Au 9.2276200000 7.2254400000 2.2847100000
Au 7.7483100000 7.2106700000 -0.2888500000
Au 4.7363600000 5.7627500000 7.3532900000
Au 7.2345300000 7.2093300000 7.3581400000
Au 5.2506600000 8.6469300000 -0.2934300000
Au 5.7596600000 10.1170800000 4.7782800000
Au 8.2554400000 8.6364000000 4.7854500000
Au 6.7281300000 8.6312800000 2.2851400000
Au 9.2237000000 10.1096000000 2.2839600000
Au 7.7487500000 10.0946400000 -0.2811000000
Au 4.7385800000 8.6456100000 7.3520900000
Au 7.2362200000 10.0940800000 7.3538100000
Au 5.2522900000 11.5299700000 -0.3000200000
Au 5.7581500000 12.9947000000 4.7763900000
Au 8.2598100000 11.5199300000 4.7792000000
Au 6.7233900000 11.5177900000 2.2840200000
Au 9.2230700000 12.9911300000 2.2810500000
Au 7.7489600000 12.9819500000 -0.2856200000
Au 4.7401100000 11.5285600000 7.3564400000
Au 7.2361200000 12.9816600000 7.3502500000
Au 5.2517700000 14.4147200000 -0.2944400000
Au 5.7568700000 15.8707300000 4.7802300000
Au 8.2590000000 14.4006800000 4.7806100000
Au 6.7264400000 14.4036600000 2.2819500000
Au 9.2244700000 15.8714000000 2.2836200000
Au 7.7492000000 15.8689600000 -0.2949300000
Au 4.7388400000 14.4131500000 7.3569400000
Au 7.2339800000 15.8689500000 7.3570400000
Au 10.2460000000 0.0018100000 -0.2893200000
Au 10.7547100000 1.4495000000 4.7809200000
Au 13.2504000000 -0.0092700000 4.7854600000
Au 11.7238200000 -0.0133700000 2.2858500000
Au 14.2186200000 1.4562900000 2.2826000000
Au 12.7448800000 1.4461400000 -0.2939100000
Au 9.7346600000 0.0003000000 7.3537500000
Au 12.2324000000 1.4457400000 7.3618700000
Au 10.2470500000 2.8862400000 -0.2957100000
Au 10.7515300000 4.3362200000 4.7816300000
Au 13.2492600000 2.8717400000 4.7788800000
Au 11.7231500000 2.8697900000 2.2837400000
Au 14.2187300000 4.3410400000 2.2784800000
Au 12.7447700000 4.3278900000 -0.2931800000
Au 9.7359600000 2.8840400000 7.3556100000
Au 12.2339600000 4.3275700000 7.3564300000
Au 10.2467700000 5.7668300000 -0.2970600000
Au 10.7520500000 7.2205600000 4.7837700000
Au 13.2478500000 5.7533900000 4.7782000000
Au 11.7251900000 5.7589100000 2.2788500000
Au 14.2196900000 7.2270800000 2.2805800000
Au 12.7432800000 7.2109500000 -0.2935100000
Au 9.7350100000 5.7636200000 7.3568200000
Au 12.2313600000 7.2097900000 7.3562800000
Au 10.2463100000 8.6456600000 -0.2971100000
Au 10.7549700000 10.1012300000 4.7819600000
Au 13.2498300000 8.6359600000 4.7805900000
Au 11.7242400000 8.6487400000 2.2792500000
Au 14.2207600000 10.1133000000 2.2813400000
Au 12.7427300000 10.0950800000 -0.2896300000
Au 9.7329400000 8.6447800000 7.3631400000
Au 12.2298000000 10.0943700000 7.3512600000
Au 10.2462000000 11.5270600000 -0.3010800000
Au 10.7571500000 12.9826700000 4.7785100000
Au 13.2527400000 11.5221500000 4.7794200000
Au 11.7225900000 11.5346600000 2.2805100000
Au 14.2225400000 12.9960300000 2.2808100000
Au 12.7429400000 12.9801700000 -0.2929100000
Au 9.7319300000 11.5278500000 7.3661100000
Au 12.2286600000 12.9788100000 7.3516000000
Au 10.2457000000 14.4147100000 -0.2946300000
Au 10.7573700000 15.8665700000 4.7795700000
Au 13.2522700000 14.4098500000 4.7833600000
Au 11.7242300000 14.4131600000 2.2820900000
Au 14.2213300000 15.8764600000 2.2843200000
Au 12.7440500000 15.8657600000 -0.2975300000
Au 9.7325100000 14.4141500000 7.3575200000
Au 12.2287300000 15.8634000000 7.3624900000
Au 15.2408400000 -0.0042100000 -0.2931700000
Au 15.7500100000 1.4670200000 4.7782700000
Au 18.2459000000 -0.0162900000 4.7834700000
Au 16.7183300000 -0.0212100000 2.2843000000
Au 19.2141900000 1.4624700000 2.2842300000
Au 17.7379800000 1.4438900000 -0.2808700000
Au 14.7285700000 -0.0054600000 7.3512100000
Au 17.2261400000 1.4442100000 7.3521900000
Au 15.2426300000 2.8791900000 -0.2989800000
Au 15.7483600000 4.3452800000 4.7765700000
Au 18.2495900000 2.8673100000 4.7785300000
Au 16.7146600000 2.8649200000 2.2836400000
Au 19.2132100000 4.3433900000 2.2809300000
Au 17.7391000000 4.3310200000 -0.2842300000
Au 14.7305400000 2.8777300000 7.3558300000
Au 17.2269200000 4.3310000000 7.3491800000
Au 15.2417200000 5.7636000000 -0.2936100000
Au 15.7477700000 7.2221700000 4.7799700000
Au 18.2484100000 5.7478800000 4.7800300000
Au 16.7173300000 5.7510100000 2.2821700000
Au 19.2136700000 7.2233700000 2.2839000000
Au 17.7403100000 7.2179400000 -0.2919700000
Au 14.7293600000 5.7623300000 7.3570700000
Au 17.2255000000 7.2178400000 7.3556300000
Au 15.2402900000 8.6469800000 -0.2873300000
Au 15.7477800000 10.1037100000 4.7816000000
Au 18.2464300000 8.6269000000 4.7833500000
Au 16.7206700000 8.6350400000 2.2844500000
Au 19.2154200000 10.1080800000 2.2843800000
Au 17.7397500000 10.1008700000 -0.2920000000
Au 14.7270500000 8.6491000000 7.3608500000
Au 17.2252800000 10.1021600000 7.3535000000
Au 15.2399200000 11.5293700000 -0.2917400000
Au 15.7483200000 12.9926200000 4.7800200000
Au 18.2450300000 11.5105200000 4.7811000000
Au 16.7224500000 11.5180900000 2.2849600000
Au 19.2182900000 12.9957500000 2.2828200000
Au 17.7383400000 12.9808900000 -0.2915800000
Au 14.7259500000 11.5328900000 7.3609400000
Au 17.2245200000 12.9817200000 7.3509600000
Au 15.2394500000 14.4136300000 -0.2923600000
Au 15.7498200000 15.8844100000 4.7801400000
Au 18.2433800000 14.3993700000 4.7823600000
Au 16.7225800000 14.3991200000 2.2833600000
Au 19.2175400000 15.8815900000 2.2859200000
Au 17.7376300000 15.8621400000 -0.2886500000
Au 14.7261100000 14.4144800000 7.3529300000
Au 17.2242700000 15.8615800000 7.3555200000
F 5.4915518479 9.9584086685 11.3380506553
O 12.9820404657 10.5646633209 11.7934314605
F 5.5581596865 9.6972988969 14.3529601736
O 10.7478904985 9.6153489502 12.3486637073
F 12.5431043747 9.5230277972 13.9613764329
S 12.2027243494 9.5029539518 12.3660225715
S 5.6612901725 8.3312547216 11.3036458117
S 5.8380122161 8.1155367523 14.0945967990
Na 8.9369064846 8.1316149245 12.4996145514
O 7.2920911988 8.0418496377 14.0644416034
O 7.0965589071 8.1711736201 11.0826972262
N 5.0940409058 7.8609781691 12.7029005364
O 4.7673240866 7.8839282840 10.2651129913
O 5.1306261009 7.4288979544 15.1349384067
N 12.8103658320 8.1070455320 11.8974925441
S 12.1657765954 6.7056421484 12.2907655891
O 10.7083554937 6.6372390648 12.2661688965
F 12.4922245519 6.5735740411 13.8865980300
O 12.9160034112 5.6563446615 11.6587514508
&END COORD
&KIND Au
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q11
&END KIND
&KIND F
BASIS_SET TZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q7
&END KIND
&KIND O
BASIS_SET TZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND C
BASIS_SET TZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q4
&END KIND
&KIND S
BASIS_SET TZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q6
&END KIND
&KIND N
BASIS_SET TZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q5
&END KIND
&KIND Na
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q9
&END KIND
&END SUBSYS
&END FORCE_EVAL
&MOTION
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1..192
&END FIXED_ATOMS
&END CONSTRAINT
&GEO_OPT
OPTIMIZER LBFGS
MAX_ITER 300
&END GEO_OPT
&END MOTION
Lucas Lodeiro
Mar 7, 2021, 11:30:18 PM3/7/21
to cp...@googlegroups.com
Hi!
As a first insight, the problem is your geometry... when the PSOLVER is not periodic, you have to put your atoms (and their density) into the box. In your case, the z axis is not periodical and all atoms and density have to be into the range 0.0 to 50.0. Your geometry has some atoms in negative coordinates... if you center by hand all positions adding 20A to all z coordinates probably your problem vanishes.
The OT scheme is not useful for metallic systems, your only choice is typical diagonalization, and the temperature of 300 K could be so small, I would try with 2000 K first, which is more close to default values into another codes as VASP and QuantumESPRESSO.
Also I add a comment from Matt Watkins in other topic:
"I normally use WAVELET poisson solver - then you need Y as the non-periodic direction (so PERIODIC XZ), the system must be in the centre of the cell and you need ~5 A vacuum each side to get converged results.The ANALYTIC psolver is also usable for 2D poisson, but it requires a much bigger cell to converge (~2x), to my knowledge.
Do check that you are converged with cell size if you go these routes. There is also a dipole correction method available somewhere (I've not used)."
Regards
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/9f833ec3-b7c3-4350-baa3-e19e0969fd6bn%40googlegroups.com.
Marcella Iannuzzi
Mar 8, 2021, 3:07:24 AM3/8/21
to cp2k
With metallic systems you need to use smearing and consequently diagonalisation.
It is not true that the smearing temperature needs to be large. If the SCF converges at 300K, this is good enough.
Also the periodic Poisson solver is good enough if you have a large vacuum space above the surface and use the dipole correction, for a not charged system.
Though your problem is the charged system, that for a metallic electronic structure is of not obvious physical interpretation.
Setting a charge to a metallic system only slightly moves the Fermi energy. For an asymmetric slab system with constrained bottom layer it is even probable that the charge is partially localized on the opposite surface.
I would guess that these are the reasons why your adsorption energy looks wrong.
Regards
Marcella
DMITRII Drugov
Mar 9, 2021, 4:24:17 AM3/9/21
to cp2k
thanks a lot. I will try your suggestions and let you know the outcome here.
Dmitrii
Reply all
Reply to author
Forward
0 new messages