Dear List I am trying to optimize an organic molecule (cation) with DZP basis and GGA psf available freely from the Simune. My input is attached very below to this mail.
Can any one tell why the program crashed even when I used Simunes' well tested DZP basis and PSF files? Simune: Are you able to reproduce this error? I use Siesta 4.1 in Linux 64. Thanks in advance Krishna ******************************************************************* ERROR MESSAGE ******************************************************************* .... .... ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: methyleneblue reinit: ----------------------------------------------------------------------- reinit: System Label: methbluegga reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Atomic number: 12 Label: C Species number: 2 Atomic number: 1 Label: H Species number: 3 Atomic number: 7 Label: N Species number: 4 Atomic number: 16 Label: S Ground state valence configuration: 3s02 Reading pseudopotential information in formatted form from C.psf Pseudopotential generated from a relativistic atomic calculation Valence configuration for pseudopotential generation: 2s( 2.00) rc: 1.01 2p( 2.00) rc: 1.28 3d( 0.00) rc: 1.60 4f( 0.00) rc: 1.60 Ground state valence configuration: 1s01 Reading pseudopotential information in formatted form from H.psf Pseudopotential generated from a relativistic atomic calculation Valence configuration for pseudopotential generation: 1s( 1.00) rc: 1.31 2p( 0.00) rc: 1.13 3d( 0.00) rc: 1.09 4f( 0.00) rc: 1.14 Ground state valence configuration: 2s02 2p03 Reading pseudopotential information in formatted form from N.psf Pseudopotential generated from a relativistic atomic calculation Valence configuration for pseudopotential generation: 2s( 2.00) rc: 1.29 2p( 3.00) rc: 1.42 3d( 0.00) rc: 1.74 4f( 0.00) rc: 2.98 Ground state valence configuration: 3s02 3p04 Reading pseudopotential information in formatted form from S.psf Pseudopotential generated from a relativistic atomic calculation Valence configuration for pseudopotential generation: 3s( 2.00) rc: 1.35 3p( 4.00) rc: 2.04 3d( 0.00) rc: 1.92 4f( 0.00) rc: 1.80 Semicore shell(s) with 2 electrons included in the valence for C For C, standard SIESTA heuristics set lmxkb to 3 (one more than the basis l, including polarization orbitals). Use PS.lmax or PS.KBprojectors blocks to override. For H, standard SIESTA heuristics set lmxkb to 2 (one more than the basis l, including polarization orbitals). Use PS.lmax or PS.KBprojectors blocks to override. For N, standard SIESTA heuristics set lmxkb to 3 (one more than the basis l, including polarization orbitals). Use PS.lmax or PS.KBprojectors blocks to override. For S, standard SIESTA heuristics set lmxkb to 3 (one more than the basis l, including polarization orbitals). Use PS.lmax or PS.KBprojectors blocks to override. <basis_specs> =============================================================================== C Z= 12 Mass= 24.310 Charge= 0.17977+309 Lmxo=2 Lmxkb= 3 BasisType=split Semic=T L=0 Nsemic=0 Cnfigmx=2 n=1 nzeta=2 polorb=0 splnorm: 0.15000 vcte: 40.000 rinn: -0.90000 qcoe: 0.0000 qyuk: 0.0000 qwid: 0.10000E-01 rcs: 5.9487 2.5090 lambdas: 1.0000 1.0000 L=1 Nsemic=0 Cnfigmx=2 n=1 nzeta=2 polorb=0 splnorm: 0.15000 vcte: 40.000 rinn: -0.90000 qcoe: 0.0000 qyuk: 0.0000 qwid: 0.10000E-01 rcs: 7.6384 2.6226 lambdas: 1.0000 1.0000 L=2 Nsemic=0 Cnfigmx=2 n=1 nzeta=1 polorb=0 splnorm: 0.15000 vcte: 40.000 rinn: -0.90000 qcoe: 6.4005 qyuk: 0.10000E-01 qwid: 0.10000E-01 rcs: 7.6384 lambdas: 1.0000 ------------------------------------------------------------------------------- L=0 Nkbl=1 erefs: 0.17977+309 L=1 Nkbl=1 erefs: 0.17977+309 L=2 Nkbl=1 erefs: 0.17977+309 L=3 Nkbl=1 erefs: 0.17977+309 =============================================================================== </basis_specs> atom: Called for C (Z = 12) read_vps: Pseudopotential generation method: read_vps: ATM4.1.0 Troullier-Martins Total valence charge: 4.00000 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: GGA Perdew, Burke & Ernzerhof 1996 V l=0 = -2*Zval/r beyond r= 1.3105 V l=1 = -2*Zval/r beyond r= 1.3437 V l=2 = -2*Zval/r beyond r= 1.5809 V l=3 = -2*Zval/r beyond r= 1.5612 All V_l potentials equal beyond r= 1.5612 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 1.5809 VLOCAL1: 99.0% of the norm of Vloc inside 17.809 Ry VLOCAL1: 99.9% of the norm of Vloc inside 40.586 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.88329 atom: Maximum radius for r*vlocal+2*Zval: 1.62091 GHOST: No ghost state for L = 0 GHOST: No ghost state for L = 1 GHOST: No ghost state for L = 2 GHOST: No ghost state for L = 3 KBgen: Kleinman-Bylander projectors: l= 0 rc= 1.725473 el= -1.010221 Ekb= 8.218425 kbcos= 0.222598 l= 1 rc= 1.725473 el= -0.388552 Ekb= -5.584060 kbcos= -0.323429 l= 2 rc= 2.055542 el= 0.001971 Ekb= -0.907290 kbcos= -0.010017 l= 3 rc= 2.300349 el= 0.003065 Ekb= -0.378353 kbcos= -0.001367 KBgen: Total number of Kleinman-Bylander projectors: 16 atom: ------------------------------------------------------------------------- atom: SANKEY-TYPE ORBITALS: atom: Selected multiple-zeta basis: split SPLIT: Orbitals with angular momentum L= 0 SPLIT: Basis orbitals for state 2s izeta = 1 lambda = 1.000000 rc = 5.948690 energy = -1.009571 kinetic = 0.879711 potential(screened) = -1.889282 potential(ionic) = -5.431187 izeta = 2 rmatch = 2.542323 splitnorm = 0.464849 energy = -0.304021 kinetic = 2.397087 potential(screened) = -2.701108 potential(ionic) = -6.677248 SPLIT: Orbitals with angular momentum L= 1 SPLIT: Basis orbitals for state 2p izeta = 1 lambda = 1.000000 rc = 7.638387 energy = -0.387791 kinetic = 2.366378 potential(screened) = -2.754169 potential(ionic) = -6.141387 izeta = 2 rmatch = 2.606692 splitnorm = 0.403257 energy = 0.178602 kinetic = 5.443206 potential(screened) = -5.264603 potential(ionic) = -9.357889 SPLIT: Orbitals with angular momentum L= 2 SPLIT: Basis orbitals for state 2d Charge confinement: Q: 6.4005 izeta = 1 lambda = 1.000000 rc = 7.638387 energy = 1.876278 kinetic = 3.712261 potential(screened) = -1.835983 potential(ionic) = -5.109537 atom: Total number of Sankey-type orbitals: 13 atm_pop: Valence configuration (for local Pseudopot. screening): 2s( 2.00) 0s( 2.00) 2p( 6.00) 0p( 0.00) 2d(10.00) 0d( 0.00) Vna: chval, zval: 18.00000 4.00000 You might have an extra low-lying basis orbital Total charge in occupied basis states different from valence charge Total charge in occupied basis states different from valence charge Stopping Program from Node: 0 Stopping Program from Node: 0 Program aborted. Backtrace: #0 0x150f52117640 in ??? #1 0x150f52118134 in ??? #2 0x150f52292f08 in ??? #3 0x7fe10a in ??? #4 0x4e5349 in vna at /home/krishnamohan/MyScience/Siesta/siesta-4.1-b4/Src/atom.F:5421 #5 0x4fcbcc in __atom_MOD_atom_main at /home/krishnamohan/MyScience/Siesta/siesta-4.1-b4/Src/atom.F:656 #6 0x44b669 in ??? #7 0x4b4567 in ??? #8 0x402bae in ??? #9 0x150f515cb349 in ??? #10 0x402c79 in ??? at ../sysdeps/x86_64/start.S:120 #11 0xffffffffffffffff in ??? Aborted (core dumped) ************************************************************************* INPUT FILE ************************************************************************** SystemName methyleneblue SystemLabel methbluegga NumberOfSpecies 4 NumberOfAtoms 38 %block ChemicalSpeciesLabel 1 12 C 2 1 H 3 7 N 4 16 S %endblock ChemicalSpeciesLabel PAO.BasisType split PAO.BasisSize DZP PAO.EnergyShift 0.02 Ry %block PAO.Basis C 3 n=2 0 2 E 40 -0.9 5.94869034392 2.5090419 n=2 1 2 E 40 -0.9 7.63838693570 2.6226139 n=2 2 1 E 40 -0.9 Q 6.4005365 .0100000 7.63838693570 H 2 n=1 0 2 E 40 -0.9 7.38657734676 2.5578156 n=1 1 1 E 40 -0.9 Q 9.4900562 1.5464743 7.38657734676 N 3 n=2 0 2 E 40 -0.9 6.5 4.3806496 n=2 1 2 E 40 -0.9 6.71294063991 2.4269315 n=2 2 1 E 40 -0.9 Q 8.2241579 .0100000 6.71294063991 S 3 n=3 0 2 E 40 -0.9 5.76834044229 3.3526650 n=3 1 2 E 40 -0.9 7.40673974180 3.5873572 n=3 2 1 E 40 -0.9 Q 2.6112698 .0100000 7.40673974180 %endblock PAO.Basis XC.Functional GGA XC.authors PBE LatticeConstant 1 Ang %block LatticeVectors 40.00000 0.000000 0.000000 0.000000 40.00000 0.000000 0.000000 0.000000 40.00000 %endblock LatticeVectors %block kgrid_Monkhorst_Pack 6 0 0 0.5 0 6 0 0.5 0 0 6 0.5 %endblock kgrid_Monkhorst_Pack AtomicCoordinatesFormat Ang %block AtomicCoordinatesAndAtomicSpecies -1.3751 -0.4797 -0.0229 1 1.3545 -0.3909 -0.0146 1 -1.1741 0.9951 0.0433 1 1.1889 0.9956 0.0470 1 -3.8132 -0.1564 -0.0134 1 3.7732 -0.1081 0.0013 1 -2.6075 -1.0066 -0.0489 1 2.6504 -0.9339 -0.0370 1 -2.4101 1.8260 0.0787 1 2.3299 1.8145 0.0849 1 -3.6360 1.3017 0.0525 1 3.6128 1.2695 0.0624 1 -5.1847 -2.1463 -0.1081 1 -6.2100 0.1677 -0.0087 1 6.1714 0.0561 -0.6161 1 5.3100 -1.9764 0.5567 1 -2.7154 -2.0853 -0.0973 2 2.7674 -2.0142 -0.0983 2 -2.2828 2.9033 0.1275 2 2.2200 2.8961 0.1355 2 -4.4809 1.9788 0.0815 2 4.4602 1.9473 0.1054 2 -4.7433 -2.6060 0.7809 2 -4.7387 -2.5245 -1.0324 2 -6.2532 -2.3785 -0.1211 2 -6.2167 0.8199 -0.8868 2 -6.2252 0.7367 0.9253 2 -7.1008 -0.4656 -0.0421 2 6.5551 0.8121 0.0769 2 5.8755 0.5438 -1.5518 2 7.0002 -0.6176 -0.8611 2 4.7795 -2.0989 1.5079 2 6.3751 -2.1211 0.7697 2 5.0014 -2.7703 -0.1315 2 -4.9874 -0.6754 -0.0415 3 5.0658 -0.6703 -0.0232 3 -0.0519 1.6424 0.0741 3 -0.0068 -1.5248 -0.0665 4 %endblock AtomicCoordinatesAndAtomicSpecies # Cation = +1 charge! NetCharge = 1. kgrid_cutoff 50.0 Ang MD.TypeOfRun CG MD.VariableCell T MD.NumCGsteps 200 MD.MaxCGDispl 0.05 Ang MD.MaxForceTol 0.005 eV/Ang # 5.d-5 eV/Ang MeshCutoff 300 Ry DM.NumberPulay 7 DM.UseSaveDM F DM.MixingWeight 0.5000 # New DM amount for next SCF cycle DM.Tolerance 1.d-6 # Tolerance in maximum difference # between input and output DM DM.NumberKick 5 DM.KickMixingWeight 1.000 DM.RequireEnergyConvergence T DM.EnergyTolerance 1.d-7 Ry ElectronicTemperature 300 K MaxSCFIterations 100 WriteCoorStep .true. WriteForces .true. WriteKpoints .false. -- **--------------------------------------------------------------------------------------------------------------** **Go Green: DO NOT print this e-mail unless absolutely necessary. Save paper, Save Trees.** *--- *Disclaimer* ---* *The information in this mail, including any attachments, is confidential and is intended solely for the addressee. Access to this mail by anyone else is unauthorized. 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