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

Lavinia ariell... at gmail.com
Mon Dec 17 06:53:50 CET 2012


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<javascript:> 
> Winterthurerstrasse 190 
> CH-8057 Zurich, Switzerland 
> --------------------------------------------------------------- 
>
> -----cp... at googlegroups.com <javascript:> wrote: ----- 
> To: cp... at googlegroups.com <javascript:> 
> From: Lavinia 
> Sent by: cp... at googlegroups.com <javascript:> 
> 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 
>       
>   -- 
>  You received this message because you are subscribed to the Google Groups 
> "cp2k" group. 
>  To view this discussion on the web visit 
> https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ. 
>   To post to this group, send email to cp... at googlegroups.com<javascript:>. 
>
>  To unsubscribe from this group, send email to 
> cp2k+... at googlegroups.com <javascript:>. 
>   For more options, visit this group at 
> http://groups.google.com/group/cp2k?hl=en. 
>    

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20121216/0d568e4d/attachment.html>


More information about the CP2K-user mailing list