[CP2K:4232] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe

Lavinia ariell... at gmail.com
Tue Jan 15 04:35:26 CET 2013


 

Dear Juerg,

 

I ran the regtest-admm for CH4 at B3LYP level (please see INPUT 1) 
successfully. Nonetheless, I get a *get_gto_basis_se*t error (please see 
ERROR) when attempting to use ADMM for my system (please see INPUT 2). I am 
not sure what causes the error. Could you please provide insight? Thank you 
for all your assistance.

 

Sincerely,

Lavinia

 

ERROR:

 

***********************************************************

 *** ERROR in get_gto_basis_set (MODULE basis_set_types) ***

 ***********************************************************

 

 *** The pointer gto_basis_set is not associated ***

 

 *** Program stopped at line number 433 of MODULE basis_set_types ***

 

 ===== Routine Calling Stack =====

 

            4 hfx_create

            3 quickstep_create_force_env

            2 qmmm_create_force_env

            1 CP2K

 

INPUT 1: 

 

&FORCE_EVAL

  METHOD Quickstep

  &DFT

    BASIS_SET_FILE_NAME ./BASIS_MOLOPT

    POTENTIAL_FILE_NAME ./GTH_POTENTIALS

    &MGRID

      CUTOFF 100

      REL_CUTOFF 30

    &END MGRID

    &QS

      METHOD GPW

      EPS_PGF_ORB 1.0E-12

   EPS_FILTER_MATRIX 0.0e0

    &END QS

    &AUXILIARY_DENSITY_MATRIX_METHOD

      METHOD BASIS_PROJECTION

      ADMM_PURIFICATION_METHOD MO_DIAG

    &END

    &POISSON

      PERIODIC NONE

      PSOLVER MT

    &END

    &SCF

      EPS_SCF 1.0E-6

      SCF_GUESS ATOMIC

      MAX_SCF 30

      &OT ON

      &END

    &END SCF

    &XC

      &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

          SCREEN_ON_INITIAL_P FALSE

        &END

        &MEMORY

          MAX_MEMORY 900

          EPS_STORAGE_SCALING 0.1

        &END

        &INTERACTION_POTENTIAL

          POTENTIAL_TYPE COULOMB

        &END

        FRACTION 0.20

      &END

    &END XC

  &END DFT

  &SUBSYS

    &CELL

      ABC 8.0 8.0 8.0 

      PERIODIC NONE

    &END CELL

    &COORD

C       0.0000       0.0000       0.0000

H       0.6297       0.6297       0.6297

H       -0.6297       -0.6297       0.6297

H       -0.6297       0.6297       -0.6297

H       0.6297       -0.6297       -0.6297

    &END COORD

    &KIND H

      BASIS_SET DZVP-MOLOPT-SR-GTH-q1

      AUX_FIT_BASIS_SET DZVP-MOLOPT-SR-GTH-q1

      POTENTIAL GTH-BLYP-q1

    &END KIND

    &KIND C

      BASIS_SET DZVP-MOLOPT-SR-GTH-q4

      AUX_FIT_BASIS_SET DZVP-MOLOPT-SR-GTH-q4

      POTENTIAL GTH-BLYP-q4

     &END KIND

  &END SUBSYS

&END FORCE_EVAL

&GLOBAL

  PROJECT CH4-BP-MO_DIAG_B3LYP

  PRINT_LEVEL LOW

  RUN_TYPE MD

  &TIMINGS

    THRESHOLD 0.000000001

  &END

&END GLOBAL

&MOTION

 &MD

    ENSEMBLE NVE

    TIMESTEP 0.5

    STEPS    2

 &END

&END

 

 

INPUT 2: 

 

@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                   GPW

# My scheme

      EPS_DEFAULT              1.0E-12

      EPS_PGF_ORB              1.0E-32

      EPS_FILTER_MATRIX        0.0E+0

    &END QS

    &AUXILIARY_DENSITY_MATRIX_METHOD

      METHOD BASIS_PROJECTION

      ADMM_PURIFICATION_METHOD MO_DIAG

    &END

    &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

          SCREEN_ON_INITIAL_P FALSE

        &END

        &MEMORY

          MAX_MEMORY  1300

          EPS_STORAGE_SCALING 1.0E-1

        &END

        &INTERACTION_POTENTIAL

          POTENTIAL_TYPE COULOMB

        &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

      AUX_FIT_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


On Thursday, December 20, 2012 11:50:41 AM UTC-5, jgh wrote:
>
> Hi 
>
> the way to get an efficient hybrid calculation is to use 
> a computer is sufficient memory in order to keep the 
> integrals in core and to use the ADMM method (see regtests). 
> Unfortunately, this is highly system dependent and needs 
> adaptation of many parameters. It is not possible to 
> give a general input. Testing on the specific system is needed. 
>
> regards 
>
> Juerg Hutter   
>
> -------------------------------------------------------------- 
> 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: 12/17/2012 07:03AM 
> Subject: Re: [CP2K:4232] GTH BLYP and B3LYP basis sets and 
> pseudopotentials for Fe 
>
> 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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