[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Rizwan Nabi
rizwan... at gmail.com
Tue Feb 10 10:16:32 UTC 2015
Hi
I want to run a job using lanthenide complexes for which i need
GTH_BASIS_SET ,as i do not have the GTH_BASIS_SET for lanthenoid metals.
Would you please provide me the GTH_BASIS_SET for the said metals or
atleast give me an idea as to how to generate GTH_BASIS_SET for the
lanthenoid metals.
Looking forward for your response.
THANKS
On Monday, December 17, 2012 at 11:23:50 AM UTC+5:30, Lavinia wrote:
>
> 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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>>
>
>
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