[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Megha Anand
meghaan... at gmail.com
Thu Sep 8 10:08:04 UTC 2016
Dear Matt,
Replacing:
&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
by
&KIND Fe
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-BLYP-q16
&END KIND
&KIND S
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-BLYP-q6
&END KIND
gives me very different energy. From the PADE PP, the energy
is: -28.4161411776336 while the one from BLYP gives the
energy: -129.19258676213. Even the energy of the reaction Fe + S --> FeS
from the BLYP PP is unphysical (4500 kJ/mol). I did not change anything
else in the input file. Surprisingly this is not the case with the sulfur.
For sulfur, with PADE PP the energy is: -9.889958274622 while with BLYP PP
it is: -9.28358433022577. For Fe, with PADE PP it is: -18.4228633044091 and
with BLYP PP it is: -121.648598758824
I wonder if it has something to do with the transition metals. Has anyone
else experience similar problems. Will someone provide information on how
to deal with transition metals in a QM calculation (non-periodic) in CP2K.
Thanks,
Megha
On Tuesday, September 6, 2016 at 6:15:53 PM UTC-4, Matt W wrote:
>
> 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
>>>>> Groups "cp2k" group.
>>>>> 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.
>>>>> To unsubscribe from this group, send email to
>>>>> cp2k+... at googlegroups.com.
>>>>> For more options, visit this group at
>>>>> http://groups.google.com/group/cp2k?hl=en.
>>>>>
>>>>
>>>>
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