[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Matt W
MattWa... at gmail.com
Tue Sep 6 22:15:52 UTC 2016
Hi,
the MOLOPT basis set is designed to go with a 18 electron pseudo potential,
so it might well give a bad result with an 8 electron one, as you use.
Also mixing pseudo potentials for with functionals that they weren't
designed for is generally not a good idea. Whilst there aren't specific
pseudos for B3LYP at the moment, it would be better to use BLYP ones than
PADE.
So changing the Fe pseudo to GTH-BLYP-q16 and the S to GTH-BLYP-q6 and see
how that affects things.
Matt
On Tuesday, September 6, 2016 at 10:17:25 PM UTC+1, Megha Anand wrote:
>
> Dear All,
>
> Are there basis sets larger than DZVP-MOLOPT-SR-GTH available for iron. I
> am trying to get energy of the reaction: Fe(g) + S(g) --> FeS(g). While the
> experimental value is ~320 kJ/mol and I am getting 268 kJ/mol. I wonder if
> small size of the basis set has anything to do with it. I am beginner with
> CP2K and not sure what could be the source of the difference. Any insights
> please. This is how my input looks like:
>
> &GLOBAL
>
> PROJECT FeS_5
>
> RUN_TYPE GEO_OPT
>
> PRINT_LEVEL MEDIUM
>
> WALLTIME 86400
>
> &END GLOBAL
>
>
> &FORCE_EVAL
>
> METHOD Quickstep
>
>
> &DFT
>
> BASIS_SET_FILE_NAME /share/apps/cp2k/cp2k/tests/QS/BASIS_MOLOPT
>
> POTENTIAL_FILE_NAME /share/apps/cp2k/cp2k/tests/QS/GTH_POTENTIALS
>
> CHARGE 0
>
> MULTIPLICITY 5
>
> UKS T
>
>
> &MGRID
>
> CUTOFF 400
>
> REL_CUTOFF 60
>
> &END MGRID
>
>
> &QS
>
> METHOD GPW
>
> EPS_DEFAULT 1.0E-12
>
> &END QS
>
>
> &SCF
>
> MAX_SCF 500
>
> &OUTER_SCF
>
> EPS_SCF 1.0E-6
>
> MAX_SCF 60
>
> &END OUTER_SCF
>
> &END SCF
>
>
> &POISSON
>
> PERIODIC NONE
>
> PSOLVER WAVELET
>
> &END POISSON
>
>
> &XC
>
> &XC_FUNCTIONAL
>
> &LYP
>
> SCALE_C 0.81
>
> &END
>
> &BECKE88
>
> SCALE_X 0.72
>
> &END
>
> &VWN
>
> FUNCTIONAL_TYPE VWN5
>
> SCALE_C 0.19
>
> &END
>
> &END XC_FUNCTIONAL
>
> &HF
>
> &SCREENING
>
> EPS_SCHWARZ 1.0E-10
>
> &END
>
> FRACTION 0.15
>
> &END
>
> &XC_GRID
>
> XC_SMOOTH_RHO NN10
>
> XC_DERIV SPLINE2_SMOOTH
>
> &END XC_GRID
>
> &END XC
>
> &END DFT
>
>
> &SUBSYS
>
> &CELL
>
> ABC 7.00 7.00 7.00
>
> PERIODIC NONE
>
> &END CELL
>
> &COORD
>
> Fe 0.0000 0.0000 0.0000
>
> S 0.0000 0.0000 1.0600
>
> &END COORD
>
> &TOPOLOGY
>
> &CENTER_COORDINATES
>
> &END
>
> &END
>
>
> &KIND Fe
>
> BASIS_SET DZVP-MOLOPT-SR-GTH
>
> POTENTIAL GTH-PADE-q8
>
> &END KIND
>
> &KIND S
>
> BASIS_SET DZVP-MOLOPT-GTH
>
> POTENTIAL GTH-PADE-q6
>
> &END KIND
>
> &END SUBSYS
>
> &END FORCE_EVAL
>
>
>
>
>
> On Tuesday, February 10, 2015 at 5:16:32 AM UTC-5, Rizwan Nabi wrote:
>>
>> 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
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
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>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ.
>>>> To post to this group, send email to cp... at googlegroups.com.
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>>>>
>>>
>>>
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