[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Lavinia
ariell... at gmail.com
Mon Dec 17 05:53:50 UTC 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
>
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