[CP2K:4249] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe

hut... at pci.uzh.ch hut... at pci.uzh.ch
Tue Jan 15 10:15:27 CET 2013


Hi

you have to define a AUX_FIT_BASIS_SET for all types.

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: 01/15/2013 04:44AM
Subject: Re: [CP2K:4249] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe

                  Dear Juerg,
   
  I ran the regtest-admm for CH4 at B3LYP level (please see INPUT 1) successfully. Nonetheless, I get a get_gto_basis_set 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 
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: 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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