Hi, You have a number of errors in your input file:
-- The atomic number of C is 6, not 12 -- For C and N, the d orbital should have n=3 -- For H the p orbital should have n=2 I hope this helps. You must have made changes to Simune's files... Alberto ----- El 2 de Feb de 2022, a las 09:49, Krishna Mohan krishna.mo...@mbcet.ac.in escribió: | 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. 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