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

hut... at pci.uzh.ch hut... at pci.uzh.ch
Thu Dec 20 17:50:41 CET 2012


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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