[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe

Rizwan Nabi rizwan... at gmail.com
Tue Feb 10 10:16:32 UTC 2015


Hi
I want to run a job using lanthenide complexes for which i need 
GTH_BASIS_SET ,as i do not have the GTH_BASIS_SET for lanthenoid metals.
Would you  please provide me the GTH_BASIS_SET for the said metals or 
atleast give me an idea as to how to generate GTH_BASIS_SET for the 
lanthenoid metals.
Looking forward for your response.
THANKS

On Monday, December 17, 2012 at 11:23:50 AM UTC+5:30, Lavinia wrote:
>
> Dear Juerg,
>
> Please suggest solutions to make B3LYP converge in a smaller number of 
> steps/iteration (~15 for BLYP relative to >40 for B3LYP) and with CPU 
> time/step/iteration comparable to BLYP (4.5s/step/iteration for BLYP 
> relative to 5400s/step/iteration for B3LYP). B3LYP calculations start 
> converging only when EPS_PGF_ORB is reduced to 1.0E-32 (as previously 
> suggested in a CP2K thread). Below you will find the input for a B3LYP 
> calculation that differs from a BLYP one only in the exchange-correlation 
> functional and EPS_PGF_ORB. Minimal sample output is also provided for both 
> BLYP and B3LYP.
>
> Input:
>
> @SET CURR_I  07
>
> @SET REPLICA  001
> @SET SEED     2000
>
> &GLOBAL
>   PROGRAM_NAME                 CP2K
>   PROJECT_NAME                 xxx_${REPLICA}_${CURR_I}
>   RUN_TYPE                     MD
>   SEED                         ${SEED}
>   PREFERRED_FFT_LIBRARY        FFTW
>   PRINT_LEVEL                  LOW
>   SAVE_MEM
> &END GLOBAL
>
> &FORCE_EVAL
>   METHOD QMMM
>   
>   &DFT
>     BASIS_SET_FILE_NAME        ./BASIS_MOLOPT
>     POTENTIAL_FILE_NAME        ./POTENTIAL
>     CHARGE                     0
>     MULTIPLICITY               1
>    
>     &SCF
>       SCF_GUESS                ATOMIC
>       EPS_SCF                  1.0E-6
>       MAX_SCF                  50
>       &OUTER_SCF
>     MAX_SCF                10
>       &END OUTER_SCF
>       &OT
> # My scheme
>         PRECONDITIONER         FULL_SINGLE_INVERSE
>         MINIMIZER              DIIS
>         N_DIIS                 7
>       &END OT
>       &PRINT
>     &RESTART
>       &EACH
>         MD                 20
>       &END EACH
>     &END RESTART
>     &RESTART_HISTORY       OFF
>     &END RESTART_HISTORY
>       &END PRINT
>     &END SCF
>
>     &QS
>       METHOD                   GAPW
> # My scheme
>       EPS_DEFAULT              1.0E-12
>       EPS_PGF_ORB              1.0E-32
>       EPS_FILTER_MATRIX        0.0E+0
>     &END QS
>     &MGRID
>       COMMENSURATE
>       CUTOFF                   300
>     &END MGRID
>     &POISSON
>       POISSON_SOLVER           MULTIPOLE
>       PERIODIC                 NONE
>       &MULTIPOLE
>          RCUT                  40
>       &END MULTIPOLE
>     &END POISSON
>     
>     &XC
>       #&XC_FUNCTIONAL           BLYP
>       #&END XC_FUNCTIONAL
>       &XC_FUNCTIONAL
>        &LYP
>          SCALE_C 0.81
>        &END
>        &BECKE88
>          SCALE_X 0.72
>        &END
>        &VWN
>          FUNCTIONAL_TYPE VWN3
>          SCALE_C 0.19
>        &END
>        &XALPHA
>          SCALE_X 0.08
>        &END
>       &END XC_FUNCTIONAL
>       &HF
>         &SCREENING
>           EPS_SCHWARZ 1.0E-10
>         &END
>         &MEMORY
>           MAX_MEMORY  512
>           EPS_STORAGE_SCALING 1.0E-1
>         &END
>         FRACTION 0.20
>       &END
>       &XC_GRID
>       XC_SMOOTH_RHO          NN10
>       XC_DERIV               SPLINE2_SMOOTH
>       &END XC_GRID
>     &END XC
>     
>     &PRINT
>       &E_DENSITY_CUBE
>     &EACH
>       MD                   20
>     &END EACH
>       &END E_DENSITY_CUBE
>     &END PRINT
>   &END DFT
>   
>   &MM
>     &FORCEFIELD
>       PARMTYPE                 CHM
>       PARM_FILE_NAME           ./par_all27_prot_na_heme.prm
>       &SPLINE
>       RCUT_NB                12.0
>       &END SPLINE
>     &END FORCEFIELD
>     &POISSON
>       &EWALD
>         EWALD_TYPE             SPME
>         ALPHA                  0.35
>         GMAX                   80 80 80
>       &END EWALD
>     &END POISSON
>   &END MM
>
>   &QMMM
>     USE_GEEP_LIB               7
>     E_COUPL                    GAUSS
>     
>     @INCLUDE run_${REPLICA}_cp2k.inp
>     
>     @INCLUDE mm_kinds
>     
>     &WALLS
>       TYPE                     REFLECTIVE
>       WALL_SKIN                1.5 1.5 1.5
>     &END WALLS
>     
>     &PRINT
>       &PROGRAM_RUN_INFO        SILENT
>       &END PROGRAM_RUN_INFO
>       &PERIODIC_INFO           SILENT
>       &END PERIODIC_INFO
>       &QMMM_LINK_INFO          SILENT
>       &END QMMM_LINK_INFO
>     &END PRINT
>   &END QMMM
>
>   &SUBSYS
>     &CELL
>       ABC                      70.125 50.266 58.796
>       PERIODIC                 XYZ
>     &END CELL
>     &TOPOLOGY
>       CONNECTIVITY             UPSF
>       CONN_FILE_NAME           ./xxx.xplor_psf
>       COORDINATE               PDB
>       COORD_FILE_NAME          ./run_${REPLICA}_cp2k.pdb
>       PARA_RES                 T
>     &END TOPOLOGY
>
>     ########################################  Basis sets and 
> pseudopotentials
>     &KIND H
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q1
>       POTENTIAL GTH-BLYP-q1
>     &END KIND
>     &KIND C
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q4
>       POTENTIAL GTH-BLYP-q4
>     &END KIND
>     &KIND N
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q5
>       POTENTIAL GTH-BLYP-q5
>     &END KIND
>     &KIND O
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q6
>       POTENTIAL GTH-BLYP-q6
>     &END KIND
>     &KIND Fe
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q16
>       POTENTIAL GTH-BLYP-q16
>     &END KIND
>   &END SUBSYS
> &END FORCE_EVAL
>
> &MOTION
>   &MD
>     ENSEMBLE                   LANGEVIN
>     STEPS                      100
>     TIMESTEP                   0.50
>     TEMPERATURE                298.15
>     &LANGEVIN
>       GAMMA 0.004
>     &END
>     &PRINT
>       &ENERGY
>         &EACH
>           MD                   20
>         &END EACH
>       &END ENERGY
>     &END PRINT
>   &END MD
>   
>   &PRINT
>     &RESTART
>       &EACH                    
>         MD                     20
>       &END EACH
>     &END RESTART
>     &RESTART_HISTORY           OFF
>     &END RESTART_HISTORY
>
>     &TRAJECTORY                SILENT
>       FORMAT                   DCD
>       &EACH
>         MD                     20
>       &END EACH
>     &END TRAJECTORY
>     &VELOCITIES                OFF
>     &END VELOCITIES
>     &FORCES                    OFF
>     &END FORCES
>   &END PRINT
> &END MOTION
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> BLYP output:
>  Decoupling Energy:                                               
> 0.0120504335
>   Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>     10 OT DIIS     0.15E+00    4.4     0.00000092      -512.9974428666 
> -1.08E-07
> *** SCF run converged in    10 steps *** 
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> B3LYP output:
> Decoupling Energy:                                               
> 0.0112659720
>   Adding QM/MM electrostatic potential to the Kohn-Sham potential.
>     41 OT DIIS     0.15E+00 5396.1     0.00039599      -514.1666899734 
> -1.87E-02
>
> Sincerely,
> Lavinia
>
> On Tuesday, August 28, 2012 3:31:11 AM UTC-4, jgh wrote:
>>
>> Hi 
>>
>> there is currently no Fe B3LYP pseudopotential. Most people 
>> would use the corresponding BLYP PP in such a case (and also 
>> for all other elements in the calculation). 
>> The best choice for a basis set is the MOLOPT series. You 
>> can find them in BASIS_MOLOPT in tests/QS. 
>>
>> Finally, you could generate your own (B3LYP) pseudos and 
>> basis sets using the atomic code that is part of CP2K. 
>> Some examples can be found in tests/ATOM. 
>>
>> regards 
>>
>> Juerg 
>>
>> -------------------------------------------------------------- 
>> Juerg Hutter                         Phone : ++41 44 635 4491 
>> Physical Chemistry Institute   FAX   : ++41 44 635 6838 
>> University of Zurich               E-mail:  hut... at pci.uzh.ch 
>> Winterthurerstrasse 190 
>> CH-8057 Zurich, Switzerland 
>> --------------------------------------------------------------- 
>>
>> -----cp... at googlegroups.com wrote: ----- 
>> To: cp... at googlegroups.com 
>> From: Lavinia 
>> Sent by: cp... at googlegroups.com 
>> Date: 08/28/2012 05:18AM 
>> Subject: [CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials 
>> for Fe 
>>
>>                   Dear GTH, 
>>     
>>   I am preparing QM(DFT)/MM calculations for a chemical reaction 
>> catalyzed by an iron enzyme. I am interested in running the simulations 
>> both at BLYP and hybrid B3LYP level. While there is a Fe GTH optimized 
>> pseudopotential generated and available for the BLYP calculations in the 
>> CP2K database, there is no Fe basis set in the GTH_BASIS_SETS. Could you 
>> provide one? Can it be generated with the new ATOM BASIS_OPTIMIZATION 
>> codebase? Would you please address the same issue for B3LYP 
>> (BASIS/PSEUDOPOTENTIAL_OPTIMIZATION availability and accuracy)? 
>>     
>>   Thank you, 
>>   LC 
>>       
>>   -- 
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>>    
>
>
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