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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Re: Problem in geometry optimization of C nanotube