[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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