GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Lavinia
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
hut...@pci.uzh.ch
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...@pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Lavinia
Sent by: cp...@googlegroups.com
Date: 08/28/2012 05:18AM
Subject: [CP2K:3995] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
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Lavinia
Dear Juerg,
Thank you so much for your reply. I have one more question. Would you recommend using only MOLOPT basis sets for all elements (Fe, H, C, N, O) for the heme protein calculations rather than a mix of a MOLOPT basis set for Fe and more diffuse GTH basis sets for the other elements?
Best regards,
Laviniahut...@pci.uzh.ch
yes, that is a good idea. You should do some testing, but I
would try the MOLOPT DZVP SR basis sets.
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Physical Chemistry Institute FAX : ++41 44 635 6838
University of Zurich E-mail: hut...@pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Lavinia
Sent by: cp...@googlegroups.com
Subject: Re: [CP2K:4000] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Lavinia
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 ${SEED}
PREFERRED_FFT_LIBRARY FFTW
PRINT_LEVEL LOW
SAVE_MEM
&END GLOBAL
&FORCE_EVAL
METHOD QMMM
&DFT
BASIS_SET_FILE_NAME ./BASIS_MOLOPT
POTENTIAL_FILE_NAME ./POTENTIAL
CHARGE 0
MULTIPLICITY 1
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-6
MAX_SCF 50
&OUTER_SCF
MAX_SCF 10
&END OUTER_SCF
&OT
# My scheme
PRECONDITIONER FULL_SINGLE_INVERSE
MINIMIZER DIIS
N_DIIS 7
&END OT
&RESTART
&EACH
MD 20
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&QS
METHOD GAPW
# My scheme
EPS_DEFAULT 1.0E-12
EPS_PGF_ORB 1.0E-32
EPS_FILTER_MATRIX 0.0E+0
&END QS
&MGRID
COMMENSURATE
CUTOFF 300
&END MGRID
&POISSON
POISSON_SOLVER MULTIPOLE
PERIODIC NONE
&MULTIPOLE
RCUT 40
&END MULTIPOLE
&END POISSON
&XC
#&XC_FUNCTIONAL BLYP
#&END XC_FUNCTIONAL
&XC_FUNCTIONAL
&LYP
SCALE_C 0.81
&END
&BECKE88
SCALE_X 0.72
&END
&VWN
FUNCTIONAL_TYPE VWN3
SCALE_C 0.19
&END
&XALPHA
SCALE_X 0.08
&END
&END XC_FUNCTIONAL
&HF
&SCREENING
EPS_SCHWARZ 1.0E-10
&END
&MEMORY
MAX_MEMORY 512
EPS_STORAGE_SCALING 1.0E-1
&END
FRACTION 0.20
&END
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
&END XC
&E_DENSITY_CUBE
&EACH
MD 20
&END EACH
&END E_DENSITY_CUBE
&END PRINT
&END DFT
&MM
&FORCEFIELD
PARMTYPE CHM
PARM_FILE_NAME ./par_all27_prot_na_heme.prm
&SPLINE
RCUT_NB 12.0
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA 0.35
GMAX 80 80 80
&END EWALD
&END POISSON
&END MM
&QMMM
USE_GEEP_LIB 7
E_COUPL GAUSS
@INCLUDE run_${REPLICA}_cp2k.inp
@INCLUDE mm_kinds
&WALLS
TYPE REFLECTIVE
WALL_SKIN 1.5 1.5 1.5
&END WALLS
&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
&ENERGY
&EACH
MD 20
&END EACH
&END ENERGY
&END PRINT
&END MD
&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:
hut...@pci.uzh.ch
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...@pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Lavinia
Sent by: cp...@googlegroups.com
Subject: Re: [CP2K:4232] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Lavinia
Dear Juerg,
I ran the regtest-admm for CH4 at B3LYP level (please see INPUT 1) successfully. Nonetheless, I get a get_gto_basis_set 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:
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
SCREEN_ON_INITIAL_P FALSE
&END
&MEMORY
MAX_MEMORY 1300
EPS_STORAGE_SCALING 1.0E-1
&END
&INTERACTION_POTENTIAL
POTENTIAL_TYPE COULOMB
AUX_FIT_BASIS_SET DZVP-MOLOPT-SR-GTH-q16
hut...@pci.uzh.ch
you have to define a AUX_FIT_BASIS_SET for all types.
regards
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Physical Chemistry Institute FAX : ++41 44 635 6838
University of Zurich E-mail: hut...@pci.uzh.ch
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Lavinia
Sent by: cp...@googlegroups.com
Subject: Re: [CP2K:4249] GTH BLYP and B3LYP basis sets and pseudopotentials for Fe
Rizwan Nabi
Megha Anand
&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
Matt W
Megha Anand
Megha Anand
&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
&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: