[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Megha Anand
meghaan... at gmail.com
Tue Sep 6 21:17:24 UTC 2016
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
>>>
>>> --
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>>
>>
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