[CP2K:4232] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Lavinia
ariell... at gmail.com
Tue Jan 15 03:35:26 UTC 2013
Dear Juerg,
I ran the regtest-admm for CH4 at B3LYP level (please see INPUT 1)
successfully. Nonetheless, I get a *get_gto_basis_se*t error (please see
ERROR) when attempting to use ADMM for my system (please see INPUT 2). I am
not sure what causes the error. Could you please provide insight? Thank you
for all your assistance.
Sincerely,
Lavinia
ERROR:
***********************************************************
*** ERROR in get_gto_basis_set (MODULE basis_set_types) ***
***********************************************************
*** The pointer gto_basis_set is not associated ***
*** Program stopped at line number 433 of MODULE basis_set_types ***
===== Routine Calling Stack =====
4 hfx_create
3 quickstep_create_force_env
2 qmmm_create_force_env
1 CP2K
INPUT 1:
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ./BASIS_MOLOPT
POTENTIAL_FILE_NAME ./GTH_POTENTIALS
&MGRID
CUTOFF 100
REL_CUTOFF 30
&END MGRID
&QS
METHOD GPW
EPS_PGF_ORB 1.0E-12
EPS_FILTER_MATRIX 0.0e0
&END QS
&AUXILIARY_DENSITY_MATRIX_METHOD
METHOD BASIS_PROJECTION
ADMM_PURIFICATION_METHOD MO_DIAG
&END
&POISSON
PERIODIC NONE
PSOLVER MT
&END
&SCF
EPS_SCF 1.0E-6
SCF_GUESS ATOMIC
MAX_SCF 30
&OT ON
&END
&END SCF
&XC
&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
SCREEN_ON_INITIAL_P FALSE
&END
&MEMORY
MAX_MEMORY 900
EPS_STORAGE_SCALING 0.1
&END
&INTERACTION_POTENTIAL
POTENTIAL_TYPE COULOMB
&END
FRACTION 0.20
&END
&END XC
&END DFT
&SUBSYS
&CELL
ABC 8.0 8.0 8.0
PERIODIC NONE
&END CELL
&COORD
C 0.0000 0.0000 0.0000
H 0.6297 0.6297 0.6297
H -0.6297 -0.6297 0.6297
H -0.6297 0.6297 -0.6297
H 0.6297 -0.6297 -0.6297
&END COORD
&KIND H
BASIS_SET DZVP-MOLOPT-SR-GTH-q1
AUX_FIT_BASIS_SET DZVP-MOLOPT-SR-GTH-q1
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-SR-GTH-q4
AUX_FIT_BASIS_SET DZVP-MOLOPT-SR-GTH-q4
POTENTIAL GTH-BLYP-q4
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT CH4-BP-MO_DIAG_B3LYP
PRINT_LEVEL LOW
RUN_TYPE MD
&TIMINGS
THRESHOLD 0.000000001
&END
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
TIMESTEP 0.5
STEPS 2
&END
&END
INPUT 2:
@SET CURR_I 07
@SET REPLICA 001
@SET SEED 2000
&GLOBAL
PROGRAM_NAME CP2K
PROJECT_NAME xxx_${REPLICA}_${CURR_I}
RUN_TYPE MD
SEED ${SEED}
PREFERRED_FFT_LIBRARY FFTW
PRINT_LEVEL LOW
SAVE_MEM
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
&DFT
BASIS_SET_FILE_NAME ./BASIS_MOLOPT
POTENTIAL_FILE_NAME ./POTENTIAL
CHARGE 0
MULTIPLICITY 1
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-6
MAX_SCF 50
&OUTER_SCF
MAX_SCF 10
&END OUTER_SCF
&OT
# My scheme
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END OT
&PRINT
&RESTART
&EACH
MD 20
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&QS
METHOD GPW
# My scheme
EPS_DEFAULT 1.0E-12
EPS_PGF_ORB 1.0E-32
EPS_FILTER_MATRIX 0.0E+0
&END QS
&AUXILIARY_DENSITY_MATRIX_METHOD
METHOD BASIS_PROJECTION
ADMM_PURIFICATION_METHOD MO_DIAG
&END
&MGRID
COMMENSURATE
CUTOFF 300
&END MGRID
&POISSON
POISSON_SOLVER MULTIPOLE
PERIODIC NONE
&MULTIPOLE
RCUT 40
&END MULTIPOLE
&END POISSON
&XC
#&XC_FUNCTIONAL BLYP
#&END XC_FUNCTIONAL
&XC_FUNCTIONAL
&LYP
SCALE_C 0.81
&END
&BECKE88
SCALE_X 0.72
&END
&VWN
FUNCTIONAL_TYPE VWN3
SCALE_C 0.19
&END
&XALPHA
SCALE_X 0.08
&END
&END XC_FUNCTIONAL
&HF
&SCREENING
EPS_SCHWARZ 1.0E-10
SCREEN_ON_INITIAL_P FALSE
&END
&MEMORY
MAX_MEMORY 1300
EPS_STORAGE_SCALING 1.0E-1
&END
&INTERACTION_POTENTIAL
POTENTIAL_TYPE COULOMB
&END
FRACTION 0.20
&END
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
&END XC
&PRINT
&E_DENSITY_CUBE
&EACH
MD 20
&END EACH
&END E_DENSITY_CUBE
&END PRINT
&END DFT
&MM
&FORCEFIELD
PARMTYPE CHM
PARM_FILE_NAME ./par_all27_prot_na_heme.prm
&SPLINE
RCUT_NB 12.0
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA 0.35
GMAX 80 80 80
&END EWALD
&END POISSON
&END MM
&QMMM
USE_GEEP_LIB 7
E_COUPL GAUSS
@INCLUDE run_${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
AUX_FIT_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
On Thursday, December 20, 2012 11:50:41 AM UTC-5, jgh wrote:
>
> Hi
>
> the way to get an efficient hybrid calculation is to use
> a computer is sufficient memory in order to keep the
> integrals in core and to use the ADMM method (see regtests).
> Unfortunately, this is highly system dependent and needs
> adaptation of many parameters. It is not possible to
> give a general input. Testing on the specific system is needed.
>
> regards
>
> Juerg Hutter
>
> --------------------------------------------------------------
> 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<javascript:>
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> ---------------------------------------------------------------
>
> -----cp... at googlegroups.com <javascript:> wrote: -----
> To: cp... at googlegroups.com <javascript:>
> From: Lavinia
> Sent by: cp... at googlegroups.com <javascript:>
> Date: 12/17/2012 07:03AM
> Subject: Re: [CP2K:4232] GTH BLYP and B3LYP basis sets and
> pseudopotentials for Fe
>
> 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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