Problem in geometry optimization of C nanotube |
- Date: 2009/01/04 17:04
- Name: Prachi
<prachiavi@gmail.com>
- I am carrying out the geometry optimization for single wall carbon nanotube (96 atoms). I am getting the first MD step correct, but for the 2nd MD step, it gives 'nan; energies . I am attaching the few lines of *.out file below.
Can you please hekp me where I am going wrong ? Thanks in advance.
# GEom opt for C-nanotube # # File Name #
System.CurrrentDirectory ./ # default=./ System.Name swnt.445 level.of.stdout 1 # default=1 (1-3) level.of.fileout 1 # default=1 (0-2) #DATA.PATH ../DFT_DATA06/
# # Definition of Atomic Species #
Species.Number 2 <Definition.of.Atomic.Species C C5.0-s2p2d1 C_PBE H H5.0-s1 H_PBE Definition.of.Atomic.Species>
# C C5.0opt2-s2p2d1 C_PBE
# # Atoms #
Atoms.Number 96 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates 1 C 2.688799 -0.353987 -5.533902 2.0 2.0 2 C 2.688799 0.353987 -4.304146 2.0 2.0 3 C 1.650961 2.151574 -5.533902 2.0 2.0 4 C 2.151574 1.650961 -4.304146 2.0 2.0 5 C -2.151574 1.650961 -5.533902 2.0 2.0 6 C 0.353987 2.688799 -5.533902 2.0 2.0 7 C -0.353987 2.688799 -4.304146 2.0 2.0 8 C -2.688799 0.353987 -5.533902 2.0 2.0 9 C -2.688799 -0.353987 -4.304146 2.0 2.0 10 C -1.650961 2.151574 -4.304146 2.0 2.0 11 C -1.650961 -2.151574 -5.533902 2.0 2.0 12 C -2.151574 -1.650961 -4.304146 2.0 2.0 13 C 2.151574 -1.650961 -5.533902 2.0 2.0 14 C -0.353987 -2.688799 -5.533902 2.0 2.0 15 C 0.353987 -2.688799 -4.304146 2.0 2.0 16 C 1.650961 -2.151574 -4.304146 2.0 2.0 17 C 2.688799 -0.353987 -3.074390 2.0 2.0 18 C 2.688799 0.353987 -1.844634 2.0 2.0 19 C 1.650961 2.151574 -3.074390 2.0 2.0 20 C 2.151574 1.650961 -1.844634 2.0 2.0 21 C -2.151574 1.650961 -3.074390 2.0 2.0 22 C 0.353987 2.688799 -3.074390 2.0 2.0 23 C -0.353987 2.688799 -1.844634 2.0 2.0 24 C -2.688799 0.353987 -3.074390 2.0 2.0 25 C -2.688799 -0.353987 -1.844634 2.0 2.0 26 C -1.650961 2.151574 -1.844634 2.0 2.0 27 C -1.650961 -2.151574 -3.074390 2.0 2.0 28 C -2.151574 -1.650961 -1.844634 2.0 2.0 29 C 2.151574 -1.650961 -3.074390 2.0 2.0 30 C -0.353987 -2.688799 -3.074390 2.0 2.0 31 C 0.353987 -2.688799 -1.844634 2.0 2.0 32 C 1.650961 -2.151574 -1.844634 2.0 2.0 33 C 2.688799 -0.353987 -0.614878 2.0 2.0 34 C 2.688799 0.353987 0.614878 2.0 2.0 35 C 1.650961 2.151574 -0.614878 2.0 2.0 36 C 2.151574 1.650961 0.614878 2.0 2.0 37 C -2.151574 1.650961 -0.614878 2.0 2.0 38 C 0.353987 2.688799 -0.614878 2.0 2.0 39 C -0.353987 2.688799 0.614878 2.0 2.0 40 C -2.688799 0.353987 -0.614878 2.0 2.0 41 C -2.688799 -0.353987 0.614878 2.0 2.0 42 C -1.650961 2.151574 0.614878 2.0 2.0 43 C -1.650961 -2.151574 -0.614878 2.0 2.0 44 C -2.151574 -1.650961 0.614878 2.0 2.0 45 C 2.151574 -1.650961 -0.614878 2.0 2.0 46 C -0.353987 -2.688799 -0.614878 2.0 2.0 47 C 0.353987 -2.688799 0.614878 2.0 2.0 48 C 1.650961 -2.151574 0.614878 2.0 2.0 49 C 2.688799 -0.353987 1.844634 2.0 2.0 50 C 2.688799 0.353987 3.074390 2.0 2.0 51 C 1.650961 2.151574 1.844634 2.0 2.0 52 C 2.151574 1.650961 3.074390 2.0 2.0 53 C -2.151574 1.650961 1.844634 2.0 2.0 54 C 0.353987 2.688799 1.844634 2.0 2.0 55 C -0.353987 2.688799 3.074390 2.0 2.0 56 C -2.688799 0.353987 1.844634 2.0 2.0 57 C -2.688799 -0.353987 3.074390 2.0 2.0 58 C -1.650961 2.151574 3.074390 2.0 2.0 59 C -1.650961 -2.151574 1.844634 2.0 2.0 60 C -2.151574 -1.650961 3.074390 2.0 2.0 61 C 2.151574 -1.650961 1.844634 2.0 2.0 62 C -0.353987 -2.688799 1.844634 2.0 2.0 63 C 0.353987 -2.688799 3.074390 2.0 2.0 64 C 1.650961 -2.151574 3.074390 2.0 2.0 65 C 2.688799 -0.353987 4.304146 2.0 2.0 66 C 2.688799 0.353987 5.533902 2.0 2.0 67 C 1.650961 2.151574 4.304146 2.0 2.0 68 C 2.151574 1.650961 5.533902 2.0 2.0 69 C -2.151574 1.650961 4.304146 2.0 2.0 70 C 0.353987 2.688799 4.304146 2.0 2.0 71 C -0.353987 2.688799 5.533902 2.0 2.0 72 C -2.688799 0.353987 4.304146 2.0 2.0 73 C -2.688799 -0.353987 5.533902 2.0 2.0 74 C -1.650961 2.151574 5.533902 2.0 2.0 75 C -1.650961 -2.151574 4.304146 2.0 2.0 76 C -2.151574 -1.650961 5.533902 2.0 2.0 77 C 2.151574 -1.650961 4.304146 2.0 2.0 78 C -0.353987 -2.688799 4.304146 2.0 2.0 79 C 0.353987 -2.688799 5.533902 2.0 2.0 80 C 1.650961 -2.151574 5.533902 2.0 2.0 81 H 2.688799 -0.194693 6.486963 0.5 0.5 82 H 2.688799 0.194693 -6.486963 0.5 0.5 83 H 1.763599 2.038936 6.486963 0.5 0.5 84 H 2.038936 1.763599 -6.486963 0.5 0.5 85 H -2.038936 1.763599 6.486963 0.5 0.5 86 H 0.194693 2.688799 6.486963 0.5 0.5 87 H -0.194693 2.688799 -6.486963 0.5 0.5 88 H -2.688799 0.194693 6.486963 0.5 0.5 89 H -2.688799 -0.194693 -6.486963 0.5 0.5 90 H -1.763599 2.038936 -6.486963 0.5 0.5 91 H -1.763599 -2.038936 6.486963 0.5 0.5 92 H -2.038936 -1.763599 -6.486963 0.5 0.5 93 H 2.038936 -1.763599 6.486963 0.5 0.5 94 H -0.194693 -2.688799 6.486963 0.5 0.5 95 H 0.194693 -2.688799 -6.486963 0.5 0.5 96 H 1.763599 -2.038936 -6.486963 0.5 0.5 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang # Ang|AU <Atoms.UnitVectors 10.00000 0.00000 0.000000 0.000000 10.0000 0.000000 0.000000 0.00000 20.00000 Atoms.UnitVectors> # # SCF or Electronic System #
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE scf.SpinPolarization off # On|Off|NC scf.ElectronicTemperature 800.0 # default=300 (K) scf.energycutoff 100.0 # default=150 (Ry) scf.maxIter 100 # default=40 scf.EigenvalueSolver cluster # DC|GDC|Cluster|Band scf.Kgrid 1 1 1 # means n1 x n2 x n3 scf.Mixing.Type Rmm-Diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk scf.Init.Mixing.Weight 0.10 # default=0.30 scf.Min.Mixing.Weight 0.01 # default=0.001 scf.Max.Mixing.Weight 0.200 # default=0.40 scf.Kerker.factor 11.0 # default=1.0 scf.Mixing.History 12 # default=5 scf.Mixing.StartPulay 2 # default=6 scf.Mixing.EveryPulay 1 # default=5 scf.criterion 1.0e-8 # default=1.0e-6 (Hartree) scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstevx scf.ExtCharge.History 4
# # 1D FFT #
1DFFT.NumGridK 900 # default=900 1DFFT.NumGridR 900 # default=900 1DFFT.EnergyCutoff 3600.0 # default=3DFFT.EnergyCutoff*3.0 (Ry)
# # Orbital Optimization #
orbitalOpt.Method Off # Off|Unrestricted|Restricted orbitalOpt.InitCoes Symmetrical # Symmetrical|Free orbitalOpt.initPrefactor 0.1 # default=0.1 orbitalOpt.scf.maxIter 100 # default=12 orbitalOpt.MD.maxIter 15 # default=5 orbitalOpt.per.MDIter 2 # default=1000000 orbitalOpt.criterion 1.0e-5 # default=1.0e-4 (Hartree/borh)^2
# # output of contracted orbitals #
CntOrb.fileout off # on|off, default=off Num.CntOrb.Atoms 1 # default=1 <Atoms.Cont.Orbitals 1 Atoms.Cont.Orbitals> # # SCF Order-N #
orderN.HoppingRanges 4.0 # default=5.0 (Ang) orderN.NumHoppings 1 # default=2
# # MD or Geometry Optimization #
MD.Type opt # Nomd|Opt|NVE|NVT_VS|NVT_NH MD.Opt.DIIS.History 5 # default=3 MD.Opt.StartDIIS 7 # default=5 MD.maxIter 100 # default=1 MD.TimeStep 1.0 MD.Opt.criterion 1.0e-5 # default=1.0e-4 (Hartree/bohr)
# # restart using a restart file, *.rst #
scf.restart off # on|off, default=off
# # Band dispersion #
Band.dispersion off # on|off, default=off # if <Band.KPath.UnitCell does not exist, # the reciprical lattice vector is employed.
# # MO output #
MO.fileout off # on|off num.HOMOs 1 # default=2 num.LUMOs 1 # default=2 MO.Nkpoint 2 # default=1 <MO.kpoint 0.0 0.0 0.0 0.0 0.0 0.2 MO.kpoint>
# # DOS and PDOS #
Dos.fileout off # on|off, default=off Dos.Erange -10.0 10.0 # default = -20 20 Dos.Kgrid 4 4 1 # default = Kgrid1 Kgrid2 Kgrid3 *********************************************************** ***********************************************************
Required cutoff energy (Ryd) for 3D-grids = 100.0000 Used cutoff energy (Ryd) for 3D-grids = 109.6941, 109.6941, 107.9598 Num. of grids of a-, b-, and c-axes = 63, 63, 125
Num.Grid1. 63 Num.Grid2. 63 Num.Grid3. 125
Cell_Volume = 13496.666074208299 (Bohr^3) GridVol = 0.027204164423 (Bohr^3) Cell vectors (bohr) of the grid cell (gtv) gtv_a = 0.299956506124, 0.000000000000, 0.000000000000 gtv_b = 0.000000000000, 0.299956506124, 0.000000000000 gtv_c = 0.000000000000, 0.000000000000, 0.302356158173 |gtv_a| = 0.299956506124 |gtv_b| = 0.299956506124 |gtv_c| = 0.302356158173
*********************************************************** *********************************************************** *********************************************************** *********************************************************** SCF history at MD= 1 *********************************************************** ***********************************************************
SCF= 1 NormRD= 1.000000000000 Uele= -3564.520142984241 SCF= 2 NormRD= 18.221733218187 Uele= -3562.830760530269 SCF= 3 NormRD= 66.673800836156 Uele= -3561.682039408528 SCF= 4 NormRD= 2.264082964810 Uele= -3560.514795814523 SCF= 5 NormRD= 0.603008928870 Uele= -3558.242907998738 SCF= 6 NormRD= 0.284237476493 Uele= -3559.373721911666 SCF= 7 NormRD= 0.115617573424 Uele= -3560.204955344595 SCF= 8 NormRD= 0.018653887543 Uele= -3561.009936565545 SCF= 9 NormRD= 0.014692960975 Uele= -3560.308539979517 SCF= 10 NormRD= 0.014727108285 Uele= -3560.613711205102 SCF= 11 NormRD= 0.014700880206 Uele= -3560.611422685562 SCF= 12 NormRD= 0.004027387977 Uele= -3560.605313886347 SCF= 13 NormRD= 0.003401373013 Uele= -3560.605969130454 SCF= 14 NormRD= 0.009032734213 Uele= -3560.308174280011 SCF= 15 NormRD= 0.008991543605 Uele= -3560.307767176931 SCF= 16 NormRD= 0.008650883244 Uele= -3560.312649444238 SCF= 17 NormRD= 0.009095358225 Uele= -3560.313431083954 SCF= 18 NormRD= 0.001391747670 Uele= -3560.601936864147 SCF= 19 NormRD= 0.003489008242 Uele= -3560.615439884013 SCF= 20 NormRD= 0.002292657600 Uele= -3560.613646527327 SCF= 21 NormRD= 0.002568893292 Uele= -3560.608068261766 SCF= 22 NormRD= 0.002749566701 Uele= -3560.605485613509 SCF= 23 NormRD= 0.013327945482 Uele= -3561.006547115375 SCF= 24 NormRD= 0.013352850841 Uele= -3561.006812550147 SCF= 25 NormRD= 0.013418136872 Uele= -3561.006981032838 SCF= 26 NormRD= 0.013619044115 Uele= -3561.007119450174 SCF= 27 NormRD= 0.013644576773 Uele= -3561.006745299399 SCF= 28 NormRD= 0.002107488984 Uele= -3560.602854488558 SCF= 29 NormRD= 0.001856505739 Uele= -3560.607532643943 SCF= 30 NormRD= 0.006641262692 Uele= -3560.312903463644 SCF= 31 NormRD= 0.002368533273 Uele= -3560.605428036523 SCF= 32 NormRD= 0.006293759210 Uele= -3560.312837306878 SCF= 33 NormRD= 0.007178724785 Uele= -3560.310478954307 SCF= 34 NormRD= 0.001433927584 Uele= -3560.616517211407 SCF= 35 NormRD= 0.001149407654 Uele= -3560.615730146949 SCF= 36 NormRD= 0.000762645290 Uele= -3560.619882333243 SCF= 37 NormRD= 0.001126054803 Uele= -3560.601429958352 SCF= 38 NormRD= 0.000949257173 Uele= -3560.603262968687 SCF= 39 NormRD= 0.000837116550 Uele= -3560.604416876862 SCF= 40 NormRD= 0.017134214125 Uele= -3560.981704487962 SCF= 41 NormRD= 0.010627510135 Uele= -3559.226784477056 SCF= 42 NormRD= 0.000680680021 Uele= -3560.609391391662 SCF= 43 NormRD= 0.007889441394 Uele= -3560.314494608556 SCF= 44 NormRD= 0.007886772200 Uele= -3560.314354051311 SCF= 45 NormRD= 0.000627421238 Uele= -3560.610379945982 SCF= 46 NormRD= 0.007987766955 Uele= -3560.314162142683 SCF= 47 NormRD= 0.008014726896 Uele= -3560.314435114953 SCF= 48 NormRD= 0.008017589665 Uele= -3560.314305575057 SCF= 49 NormRD= 0.010629885725 Uele= -3559.225190003765 SCF= 50 NormRD= 0.008220301541 Uele= -3560.310327124282 SCF= 51 NormRD= 0.007053927879 Uele= -3560.314666484736 SCF= 52 NormRD= 0.000701495245 Uele= -3560.610477103965 SCF= 53 NormRD= 0.006860778062 Uele= -3560.314217978922 SCF= 54 NormRD= 0.006835309500 Uele= -3560.314217318591 SCF= 55 NormRD= 0.006820387537 Uele= -3560.314169171857 SCF= 56 NormRD= 0.006799074296 Uele= -3560.314100178555 SCF= 57 NormRD= 0.006871304880 Uele= -3560.314338532565 SCF= 58 NormRD= 0.001741995792 Uele= -3560.606048407487 SCF= 59 NormRD= 0.001492499098 Uele= -3560.606981125170 SCF= 60 NormRD= 0.003361499068 Uele= -3560.619348496761 SCF= 61 NormRD= 0.003368503681 Uele= -3560.619473426314 SCF= 62 NormRD= 0.002205881431 Uele= -3560.606133803738 SCF= 63 NormRD= 0.007813434078 Uele= -3560.310210562442 SCF= 64 NormRD= 0.001872221636 Uele= -3560.607711979662 SCF= 65 NormRD= 0.001173912411 Uele= -3560.610687784890 SCF= 66 NormRD= 0.001273963699 Uele= -3560.610182015621 SCF= 67 NormRD= 0.001365136897 Uele= -3560.609522411204 SCF= 68 NormRD= 0.001238438145 Uele= -3560.610617741200 SCF= 69 NormRD= 0.001921362392 Uele= -3560.604298108075 SCF= 70 NormRD= 0.006447856688 Uele= -3560.314328680650 SCF= 71 NormRD= 0.001977766390 Uele= -3560.605092636395 SCF= 72 NormRD= 0.001859402509 Uele= -3560.606537862785 SCF= 73 NormRD= 0.001718517784 Uele= -3560.607209312605 SCF= 74 NormRD= 0.001740827889 Uele= -3560.607053238277 SCF= 75 NormRD= 0.001628203198 Uele= -3560.607495634602 SCF= 76 NormRD= 0.010569310639 Uele= -3559.225014761214 SCF= 77 NormRD= 0.010569322775 Uele= -3559.225006431312 SCF= 78 NormRD= 0.010560206798 Uele= -3559.224914810282 SCF= 79 NormRD= 0.010554433851 Uele= -3559.224914871289 SCF= 80 NormRD= 0.010567789805 Uele= -3559.224904866234 SCF= 81 NormRD= 0.010581411164 Uele= -3559.225072029330 SCF= 82 NormRD= 0.007928448224 Uele= -3560.309992272137 SCF= 83 NormRD= 0.001002190015 Uele= -3560.609798396702 SCF= 84 NormRD= 0.000925502431 Uele= -3560.610060084498 SCF= 85 NormRD= 0.000886767271 Uele= -3560.610196021277 SCF= 86 NormRD= 0.006766132932 Uele= -3560.313982426452 SCF= 87 NormRD= 0.006803998702 Uele= -3560.314081082282 SCF= 88 NormRD= 0.000751382157 Uele= -3560.610698477780 SCF= 89 NormRD= 0.000900771296 Uele= -3560.610140543718 SCF= 90 NormRD= 0.001057613231 Uele= -3560.609551215178 SCF= 91 NormRD= 0.006969125827 Uele= -3560.314478659545 SCF= 92 NormRD= 0.007519564980 Uele= -3560.315848030399 SCF= 93 NormRD= 0.007461452498 Uele= -3560.315697996144 SCF= 94 NormRD= 0.007530655555 Uele= -3560.315871904627 SCF= 95 NormRD= 0.007977825238 Uele= -3560.310147800723 SCF= 96 NormRD= 0.007309527075 Uele= -3560.315318506385 SCF= 97 NormRD= 0.007164663430 Uele= -3560.314963574998 SCF= 98 NormRD= 0.007207214897 Uele= -3560.315067393586 SCF= 99 NormRD= 0.006959479527 Uele= -3560.314474960787 SCF= 100 NormRD= 0.000772306122 Uele= -3560.610698246540
******************************************************* Total energy (Hartree) at MD = 1 *******************************************************
Uele. -3560.610698246540
Ukin. 8.587684443417 UH0. -4246.479725532720 UH1. 1303.544881522591 Una. -13838.364066796177 Unl. 10337.378321322072 Uxc0. -3.281976666447 Uxc1. -3.281976666447 Ucore. 3931.684347292305 Uhub. 0.000000000000 Ucs. 0.000000000000 Uzs. 0.000000000000 Uzo. 0.000000000000 Uef. 0.000000000000 Utot. -2510.212511081405
Note:
Utot = Ukin+UH0+UH1+Una+Unl+Uxc0+Uxc1+Ucore+Uhub+Ucs+Uzs+Uzo+Uef
Uene: band energy Ukin: kinetic energy UH0: electric part of screened Coulomb energy UH1: difference electron-electron Coulomb energy Una: neutral atom potential energy Unl: non-local potential energy Uxc0: exchange-correlation energy for alpha spin Uxc1: exchange-correlation energy for beta spin Ucore: core-core Coulomb energy Uhub: LDA+U energy Ucs: constraint energy for spin orientation Uzs: Zeeman term for spin magnetic moment Uzo: Zeeman term for orbital magnetic moment Uef: electric energy by electric field
(see also PRB 72, 045121(2005) for the energy contributions)
Chemical potential (Hartree) -0.035109352576
*********************************************************** *********************************************************** SCF history at MD= 2 *********************************************************** ***********************************************************
SCF= 1 NormRD= 1.000000000000 Uele= -1840.358963080547 SCF= 2 NormRD= 1.153552255145 Uele= 0.000000000000 SCF= 3 NormRD= 3.593875145140 Uele= 0.000000000000
******************************************************* Total energy (Hartree) at MD = 2 *******************************************************
Uele. 0.000000000000
Ukin. nan UH0. -3551.852979487085 UH1. 720.823651605693 Una. 0.000000000000 Unl. 0.000000000000 Uxc0. 0.000000000000 Uxc1. 0.000000000000 Ucore. 3286.755381688088 Uhub. 0.000000000000 Ucs. 0.000000000000 Uzs. 0.000000000000 Uzo. 0.000000000000 Uef. 0.000000000000 Utot. nan
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