[CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe

Megha Anand meghaan... at gmail.com
Wed Sep 7 00:32:26 CEST 2016


Thanks Matt! I will incorporate your suggestions.

Best regards,
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 
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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. 
>>>>>  To unsubscribe from this group, send email to 
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>>>>>   For more options, visit this group at 
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>>>>>    
>>>>
>>>>
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