<div dir="ltr">Dear Matt,<div> </div><div>Replacing:</div><div> </div><div> &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</div><div> </div><div>by</div><div> </div><div> &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</div><div> On Tuesday, September 6, 2016 at 6:15:53 PM UTC-4, Matt W wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi,<div> </div><div>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.</div><div> </div><div>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.</div><div> </div><div>So changing the Fe pseudo to GTH-BLYP-q16 and the S to GTH-BLYP-q6 and see how that affects things.</div><div> </div><div>Matt</div><div> On Tuesday, September 6, 2016 at 10:17:25 PM UTC+1, Megha Anand wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear All,<div> </div><div>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:</div><div> </div><div> &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</div><div> </div><div> </div><div> </div><div> </div> <div> On Tuesday, February 10, 2015 at 5:16:32 AM UTC-5, Rizwan Nabi wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi<div>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.</div><div>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.</div><div>Looking forward for your response.</div><div>THANKS On Monday, December 17, 2012 at 11:23:50 AM UTC+5:30, Lavinia wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">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:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">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: <a>hut...@pci.uzh.ch</a> Winterthurerstrasse 190 CH-8057 Zurich, Switzerland --------------------------------------------------------------- -----<a>cp...@googlegroups.com</a> wrote: ----- To: <a>cp...@googlegroups.com</a> From: Lavinia Sent by: <a>cp...@googlegroups.com</a> 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 Groups "cp2k" group. To view this discussion on the web visit <a href="https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ" rel="nofollow" target="_blank" onmousedown="this.href='https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ';return true;" onclick="this.href='https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ';return true;">https://groups.google.com/d/msg/cp2k/-/uXrQisPvBLEJ</a>. To post to this group, send email to <a>cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a>cp2k+...@googlegroups.com</a>. 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