[Smeagol-discuss] Smeagol-discuss Digest, Vol 18, Issue 4
asa aravindh
mails2asa at gmail.com
Mon Jun 8 11:24:50 IST 2009
Hi..
I think there is a problem in the memory allocation. Try with more number of
processors
But I am not sure..
Asa
On Mon, Jun 8, 2009 at 1:54 PM,
<smeagol-discuss-request at lists.tchpc.tcd.ie>wrote:
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> Today's Topics:
>
> 1. segmentation fault (???)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 4 Jun 2009 16:21:47 -0400
> From: ??? <mjkim9799 at gmail.com>
> Subject: [Smeagol-discuss] segmentation fault
> To: smeagol-discuss at lists.tchpc.tcd.ie
> Message-ID:
> <936bdfc10906041321y4859c147g6c9d15e5f3335a4e at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear folks
>
> Does anyone have an idea for this or this kind of error?
> This happened at the start of MD step.
> The lead calculation has been done well.
> Two input file and output file are attached.
>
> Thank you,
>
> Joonho
>
>
> initatomlists: Number of atoms, orbitals, and projectors: 92 220
> 498
> siesta: System type = bulk
> * Maximum dynamic memory allocated = 3 MB
> siesta: ===============================
> SMEAGOL Bias step = 0, V = 0.000 Ry
> Begin CG move = 0
> ===============================
> InitMesh: MESH = 72 x 72 x 250 = 1296000
> InitMesh: Mesh cutoff (required, used) = 180.000 184.786 Ry
> * Maximum dynamic memory allocated = 128 MB
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> smeagol 0000000000666E87 Unknown Unknown Unknown
> smeagol 00000000006667AB Unknown Unknown Unknown
> smeagol 00000000005F19C2 Unknown Unknown Unknown
> smeagol 0000000000656838 Unknown Unknown Unknown
> smeagol 000000000065E0D3 Unknown Unknown Unknown
> smeagol 000000000058219C Unknown Unknown Unknown
> smeagol 0000000000403DAC Unknown Unknown Unknown
> libc.so.6 0000003BE721D8A4 Unknown Unknown Unknown
> smeagol 0000000000403CB9 Unknown Unknown Unknown
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.tchpc.tcd.ie/pipermail/smeagol-discuss/attachments/20090604/42cad06e/attachment.html
> -------------- next part --------------
> SIESTA 1.3.7 -- [1.3f1 release] (04 Feb 2004)
> Architecture : intel-mkl
> Compiler flags:
> SERIAL version
>
> * Running in serial mode
> >> Start of run: 4-JUN-2009 16:57:34
>
> ***********************
> * WELCOME TO SIESTA *
> ***********************
>
> reinit: Reading from standard input
> ************************** Dump of input data file
> ****************************
> SystemName DT1
> SystemLabel DT1_tr
> NumberOfAtoms 92
> NumberOfSpecies 4
> %block ChemicalSpeciesLabel
> 1 1 H
> 2 6 C
> 3 16 S
> 4 79 Au
> %endblock ChemicalSpeciesLabel
> PAO.BasisSize DZP
> PAO.BasisType split
> PAO.EnergyShift 100 meV
> PAO.SplitNorm 0.150
> %block PAO.Basis
> Au 1
> n=6 0 1
> 6.0
> %endblock PAO.Basis
> #%block PAO.BasisSizes
> # S SZ
> # C SZ
> # H SZ
> # Au SZ
> #%endblock PAO.BasisSizes
> LatticeConstant 1. Ang
> %block LatticeVectors
> 8.1572 0.0000 0.0000 1
> 0.0000 8.1572 0.0000 1
> 0.0000 0.0000 30.5743 1
> %endblock LatticeVectors
> AtomicCoordinatesFormat Ang
> %block AtomicCoordinatesAndAtomicSpecies
> 0.0000 0.0000 0.0000 4
> 0.0000 4.0786 0.0000 4
> 2.0393 2.0393 0.0000 4
> 2.0393 6.1179 0.0000 4
> 4.0786 0.0000 0.0000 4
> 4.0786 4.0786 0.0000 4
> 6.1179 2.0393 0.0000 4
> 6.1179 6.1179 0.0000 4
> 0.0000 2.0393 2.0393 4
> 0.0000 6.1179 2.0393 4
> 2.0393 0.0000 2.0393 4
> 2.0393 4.0786 2.0393 4
> 4.0786 2.0393 2.0393 4
> 4.0786 6.1179 2.0393 4
> 6.1179 0.0000 2.0393 4
> 6.1179 4.0786 2.0393 4
> 0.0000 0.0000 4.0786 4
> 0.0000 4.0786 4.0786 4
> 2.0393 2.0393 4.0786 4
> 2.0393 6.1179 4.0786 4
> 4.0786 0.0000 4.0786 4
> 4.0786 4.0786 4.0786 4
> 6.1179 2.0393 4.0786 4
> 6.1179 6.1179 4.0786 4
> 0.0000 2.0393 6.1179 4
> 0.0000 6.1179 6.1179 4
> 2.0393 0.0000 6.1179 4
> 2.0393 4.0786 6.1179 4
> 4.0786 2.0393 6.1179 4
> 4.0786 6.1179 6.1179 4
> 6.1179 0.0000 6.1179 4
> 6.1179 4.0786 6.1179 4
> 0.0000 0.0000 8.1572 4
> 0.0000 4.0786 8.1572 4
> 2.0393 2.0393 8.1572 4
> 2.0393 6.1179 8.1572 4
> 4.0786 0.0000 8.1572 4
> 4.0786 4.0786 8.1572 4
> 6.1179 2.0393 8.1572 4
> 6.1179 6.1179 8.1572 4
> -0.0660 0.0280 10.1965 3
> 0.0640 -1.4990 12.7945 3
> -0.0260 0.0460 11.9315 2
> -0.0720 1.1300 12.8205 2
> -0.0370 0.7040 14.1762 2
> 0.0360 -0.7010 14.3535 2
> 0.0710 -1.1280 15.7117 2
> 0.0250 -0.0420 16.6025 2
> -0.0650 1.5030 15.7385 3
> 0.1290 -2.1950 16.0275 1
> -0.1300 2.1990 12.5085 1
> 0.0650 -0.0230 18.3385 3
> 0.0000 0.0000 20.3778 4
> 0.0000 4.0786 20.3778 4
> 2.0393 2.0393 20.3778 4
> 2.0393 6.1179 20.3778 4
> 4.0786 0.0000 20.3778 4
> 4.0786 4.0786 20.3778 4
> 6.1179 2.0393 20.3778 4
> 6.1179 6.1179 20.3778 4
> 0.0000 2.0393 22.4171 4
> 0.0000 6.1179 22.4171 4
> 2.0393 0.0000 22.4171 4
> 2.0393 4.0786 22.4171 4
> 4.0786 2.0393 22.4171 4
> 4.0786 6.1179 22.4171 4
> 6.1179 0.0000 22.4171 4
> 6.1179 4.0786 22.4171 4
> 0.0000 0.0000 24.4564 4
> 0.0000 4.0786 24.4564 4
> 2.0393 2.0393 24.4564 4
> 2.0393 6.1179 24.4564 4
> 4.0786 0.0000 24.4564 4
> 4.0786 4.0786 24.4564 4
> 6.1179 2.0393 24.4564 4
> 6.1179 6.1179 24.4564 4
> 0.0000 2.0393 26.4957 4
> 0.0000 6.1179 26.4957 4
> 2.0393 0.0000 26.4957 4
> 2.0393 4.0786 26.4957 4
> 4.0786 2.0393 26.4957 4
> 4.0786 6.1179 26.4957 4
> 6.1179 0.0000 26.4957 4
> 6.1179 4.0786 26.4957 4
> 0.0000 0.0000 28.5350 4
> 0.0000 4.0786 28.5350 4
> 2.0393 2.0393 28.5350 4
> 2.0393 6.1179 28.5350 4
> 4.0786 0.0000 28.5350 4
> 4.0786 4.0786 28.5350 4
> 6.1179 2.0393 28.5350 4
> 6.1179 6.1179 28.5350 4
> %endblock AtomicCoordinatesAndAtomicSpecies
> #kgrid_cutoff 0. Ang
> #%block kgrid_Monkhorst_Pack
> # 10 0 0 0.0
> # 0 10 0 0.0
> # 0 0 10 0.0
> #%endblock kgrid_Monkhorst_Pack
> XC.functional GGA # LDA or GGA
> XC.authors PBE # CA for LDA, PBE for GGA
> SpinPolarized F
> FixSpin F
> TotalSpin 0.0
> NonCollinearSpin F
> MeshCutoff 180. Ry
> MaxSCFIterations 500
> DM.MixingWeight 0.1
> DM.NumberPulay 5 # Pulay convergency accelerator
> DM.MixSCF1 F
> DM.PulayOnFile F # Store in memory (F) or in files (T)
> DM.Tolerance 1.0E-4
> NeglNonOverlapInt T # F do not neglect
> #SolutionMethod diagon
> ElectronicTemperature 300 K # Default value
> DM.UseSaveDM F # T if scf does not converge
> DM.MixSCF1 F
> WriteCoorXmol T
> SaveElectrostaticPotential T
> SaveHS F # Save the Hamiltonian and Overlap
> matrices
> SaveRho T # Save the valence pseudocharge
> density
> SaveDeltaRho F
> WriteDenchar F # Write Denchar output
> WriteDMT T
> WriteEigenvalues F
> WriteMullikenPop 1
> EMTransport T
> NEnergReal 1000
> NEnergImCircle 200
> NEnergImLine 50
> NPoles 20
> VInitial 0.d0 eV
> VFinal 3.d0 eV
> NIVPoints 30
> Delta 1.d-5
> EnergLowestBound -1.4d0 Ry
> NSlices 1
> TrCoefficients T
> AtomLeftVCte 2
> AtomRightVCte 7
> NTransmPoints 800
> InitTransmRange 1.0d0 Ry
> FinalTransmRange 1.8d0 Ry
> PeriodicTransp T
> InitTransport F
> HartreeLeadsBottom -6.92388439 eV
> HartreeLeadsLeft 0.0000 Ang
> HartreeLeadsRight 30.5743 Ang
> #%block LocalDensityOfStates
> # 1.400d0 1.470d0 Ry
> #%endblock LocalDensityOfStates
> %block SaveBiasSteps
> 0 1
> %endblock SaveBiasSteps
> ************************** End of input data file
> *****************************
>
> reinit:
> -----------------------------------------------------------------------
> reinit: System Name: DT1
> reinit:
> -----------------------------------------------------------------------
> reinit: System Label: DT1_tr
> reinit:
> -----------------------------------------------------------------------
>
> initatom: Reading input for the pseudopotentials and atomic orbitals
> ----------
> Species number: 1 Label: H Atomic number: 1
> Species number: 2 Label: C Atomic number: 6
> Species number: 3 Label: S Atomic number: 16
> Species number: 4 Label: Au Atomic number: 79
> Ground state valence configuration: 1s01
> Reading pseudopotential information in formatted form from H.psf
> Ground state valence configuration: 2s02 2p02
> Reading pseudopotential information in formatted form from C.psf
> Ground state valence configuration: 3s02 3p04
> Reading pseudopotential information in formatted form from S.psf
> Ground state valence configuration: 6s01 5d10
> Reading pseudopotential information in formatted form from Au.psf
> 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 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 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.
> For Au, standard SIESTA heuristics set lmxkb to 1
> (one more than the basis l, including polarization orbitals).
> Use PS.lmax or PS.KBprojectors blocks to override.
>
> <basis_specs>
>
> ===============================================================================
> H Z= 1 Mass= 1.0100 Charge= 0.0000
> Lmxo=0 Lmxkb=2 BasisType=split Semic=F
> L=0 Nsemic=0 Cnfigmx=1
> n=1 nzeta=2 polorb=1
> vcte: 0.0000
> rinn: 0.0000
> rcs: 0.0000 0.0000
> lambdas: 1.0000 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
>
> ===============================================================================
> </basis_specs>
>
> atom: Called for H (Z = 1)
>
> read_vps: Pseudopotential generation method:
> read_vps: ATM 3.2.2 Troullier-Martins
>
> read_vps: Valence configuration (pseudopotential and basis set generation):
> 1s( 1.00) rc: 1.33
> 2p( 0.00) rc: 1.33
> 3d( 0.00) rc: 0.37
> Total valence charge: 1.00000
>
> xc_check: Exchange-correlation functional:
> xc_check: GGA Perdew, Burke & Ernzerhof 1996
> V l=0 = -2*Zval/r beyond r= 1.2656
> V l=1 = -2*Zval/r beyond r= 1.2498
> V l=2 = -2*Zval/r beyond r= 0.3563
> All V_l potentials equal beyond r= 1.2656
> This should be close to max(r_c) in ps generation
> All pots = -2*Zval/r beyond r= 1.2656
>
> VLOCAL1: 99.0% of the norm of Vloc inside 27.100 Ry
> VLOCAL1: 99.9% of the norm of Vloc inside 61.762 Ry
> atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.48935
> atom: Maximum radius for r*vlocal+2*Zval: 1.24984
> GHOST: No ghost state for L = 0
> GHOST: No ghost state for L = 1
> GHOST: No ghost state for L = 2
>
> KBgen: Kleinman-Bylander projectors:
> l= 0 rc= 1.398961 el= -0.477209 Ekb= -2.001853 kbcos= -0.352188
> l= 1 rc= 1.470814 el= 0.001006 Ekb= -0.423408 kbcos= -0.024395
> l= 2 rc= 1.489346 el= 0.001895 Ekb= -0.481957 kbcos= -0.001574
>
> KBgen: Total number of Kleinman-Bylander projectors: 9
> atom:
> -------------------------------------------------------------------------
>
> atom: SANKEY-TYPE ORBITALS:
> atom: Selected multiple-zeta basis: split
>
> SPLIT: Orbitals with angular momentum L= 0
>
> SPLIT: Basis orbitals for state 1s
>
> SPLIT: PAO cut-off radius determinated from an
> SPLIT: energy shift= 0.007350 Ry
>
> izeta = 1
> lambda = 1.000000
> rc = 5.471469
> energy = -0.469881
> kinetic = 0.917247
> potential(screened) = -1.387128
> potential(ionic) = -1.910176
>
> izeta = 2
> rmatch = 3.952598
> splitnorm = 0.150000
> energy = -0.376910
> kinetic = 1.452740
> potential(screened) = -1.829649
> potential(ionic) = -2.377172
>
> POLgen: Perturbative polarization orbital with L= 1
>
> POLgen: Polarization orbital for state 1s
>
> izeta = 1
> rc = 5.471469
> energy = 0.628146
> kinetic = 1.274519
> potential(screened) = -0.646373
> potential(ionic) = -1.124360
> atom: Total number of Sankey-type orbitals: 5
>
> atm_pop: Valence configuration(local Pseudopot. screening):
> 1s( 1.00)
> Vna: chval, zval: 1.00000 1.00000
>
> Vna: Cut-off radius for the neutral-atom potential: 5.471469
>
> atom:
> _________________________________________________________________________
>
> <basis_specs>
>
> ===============================================================================
> C Z= 6 Mass= 12.010 Charge= 0.0000
> Lmxo=1 Lmxkb=3 BasisType=split Semic=F
> L=0 Nsemic=0 Cnfigmx=2
> n=1 nzeta=2 polorb=0
> vcte: 0.0000
> rinn: 0.0000
> rcs: 0.0000 0.0000
> lambdas: 1.0000 1.0000
> L=1 Nsemic=0 Cnfigmx=2
> n=1 nzeta=2 polorb=1
> vcte: 0.0000
> rinn: 0.0000
> rcs: 0.0000 0.0000
> lambdas: 1.0000 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 = 6)
>
> read_vps: Pseudopotential generation method:
> read_vps: ATM 3.2.2 Troullier-Martins
>
> read_vps: Valence configuration (pseudopotential and basis set generation):
> 2s( 2.00) rc: 1.56
> 2p( 2.00) rc: 1.56
> 3d( 0.00) rc: 1.56
> 4f( 0.00) rc: 1.56
> Total valence charge: 4.00000
>
> xc_check: Exchange-correlation functional:
> xc_check: GGA Perdew, Burke & Ernzerhof 1996
> V l=0 = -2*Zval/r beyond r= 1.5227
> V l=1 = -2*Zval/r beyond r= 1.5227
> V l=2 = -2*Zval/r beyond r= 1.5227
> V l=3 = -2*Zval/r beyond r= 1.5227
> All V_l potentials equal beyond r= 1.4851
> This should be close to max(r_c) in ps generation
> All pots = -2*Zval/r beyond r= 1.5227
>
> VLOCAL1: 99.0% of the norm of Vloc inside 19.682 Ry
> VLOCAL1: 99.9% of the norm of Vloc inside 44.856 Ry
> atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.79142
> atom: Maximum radius for r*vlocal+2*Zval: 1.54183
> 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= 1.661951 el= -1.010689 Ekb= 5.289847 kbcos= 0.316429
> l= 1 rc= 1.661951 el= -0.388490 Ekb= -4.102504 kbcos= -0.351025
> l= 2 rc= 1.747182 el= 0.001971 Ekb= -1.006005 kbcos= -0.008530
> l= 3 rc= 1.791422 el= 0.003065 Ekb= -0.421399 kbcos= -0.001072
>
> 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
>
> SPLIT: PAO cut-off radius determinated from an
> SPLIT: energy shift= 0.007350 Ry
>
> izeta = 1
> lambda = 1.000000
> rc = 4.632753
> energy = -1.003183
> kinetic = 0.861066
> potential(screened) = -1.864249
> potential(ionic) = -5.446202
>
> izeta = 2
> rmatch = 3.431921
> splitnorm = 0.150000
> energy = -0.867709
> kinetic = 1.310999
> potential(screened) = -2.178708
> potential(ionic) = -6.002100
>
> SPLIT: Orbitals with angular momentum L= 1
>
> SPLIT: Basis orbitals for state 2p
>
> SPLIT: PAO cut-off radius determinated from an
> SPLIT: energy shift= 0.007350 Ry
>
> izeta = 1
> lambda = 1.000000
> rc = 5.658549
> energy = -0.380916
> kinetic = 2.410776
> potential(screened) = -2.791692
> potential(ionic) = -6.235107
>
> izeta = 2
> rmatch = 3.653288
> splitnorm = 0.150000
> energy = -0.248957
> kinetic = 3.560897
> potential(screened) = -3.809854
> potential(ionic) = -7.627676
>
> POLgen: Perturbative polarization orbital with L= 2
>
> POLgen: Polarization orbital for state 2p
>
> izeta = 1
> rc = 5.658549
> energy = 1.109759
> kinetic = 2.301035
> potential(screened) = -1.191276
> potential(ionic) = -4.010213
> atom: Total number of Sankey-type orbitals: 13
>
> atm_pop: Valence configuration(local Pseudopot. screening):
> 2s( 2.00)
> 2p( 2.00)
> Vna: chval, zval: 4.00000 4.00000
>
> Vna: Cut-off radius for the neutral-atom potential: 5.658549
>
> atom:
> _________________________________________________________________________
>
> <basis_specs>
>
> ===============================================================================
> S Z= 16 Mass= 32.070 Charge= 0.0000
> Lmxo=1 Lmxkb=3 BasisType=split Semic=F
> L=0 Nsemic=0 Cnfigmx=3
> n=1 nzeta=2 polorb=0
> vcte: 0.0000
> rinn: 0.0000
> rcs: 0.0000 0.0000
> lambdas: 1.0000 1.0000
> L=1 Nsemic=0 Cnfigmx=3
> n=1 nzeta=2 polorb=1
> vcte: 0.0000
> rinn: 0.0000
> rcs: 0.0000 0.0000
> lambdas: 1.0000 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 S (Z = 16)
>
> read_vps: Pseudopotential generation method:
> read_vps: ATM 3.2.2 Troullier-Martins
>
> read_vps: Valence configuration (pseudopotential and basis set generation):
> 3s( 2.00) rc: 1.63
> 3p( 4.00) rc: 1.76
> 3d( 0.00) rc: 1.94
> 4f( 0.00) rc: 1.94
> Total valence charge: 6.00000
>
> xc_check: Exchange-correlation functional:
> xc_check: GGA Perdew, Burke & Ernzerhof 1996
> V l=0 = -2*Zval/r beyond r= 1.5917
> V l=1 = -2*Zval/r beyond r= 1.7157
> V l=2 = -2*Zval/r beyond r= 1.8962
> V l=3 = -2*Zval/r beyond r= 1.8962
> All V_l potentials equal beyond r= 1.8962
> This should be close to max(r_c) in ps generation
> All pots = -2*Zval/r beyond r= 1.8962
>
> VLOCAL1: 99.0% of the norm of Vloc inside 12.073 Ry
> VLOCAL1: 99.9% of the norm of Vloc inside 27.515 Ry
> atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.28723
> atom: Maximum radius for r*vlocal+2*Zval: 1.99338
> 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= 2.095595 el= -1.268692 Ekb= 6.979923 kbcos= 0.305692
> l= 1 rc= 2.148649 el= -0.515299 Ekb= 2.191479 kbcos= 0.305687
> l= 2 rc= 2.148649 el= 0.001998 Ekb= -3.071052 kbcos= -0.051783
> l= 3 rc= 2.230759 el= 0.003105 Ekb= -0.881646 kbcos= -0.003826
>
> 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 3s
>
> SPLIT: PAO cut-off radius determinated from an
> SPLIT: energy shift= 0.007350 Ry
>
> izeta = 1
> lambda = 1.000000
> rc = 4.606082
> energy = -1.261626
> kinetic = 0.866936
> potential(screened) = -2.128562
> potential(ionic) = -7.124217
>
> izeta = 2
> rmatch = 3.542623
> splitnorm = 0.150000
> energy = -1.111372
> kinetic = 1.365375
> potential(screened) = -2.476748
> potential(ionic) = -7.712264
>
> SPLIT: Orbitals with angular momentum L= 1
>
> SPLIT: Basis orbitals for state 3p
>
> SPLIT: PAO cut-off radius determinated from an
> SPLIT: energy shift= 0.007350 Ry
>
> izeta = 1
> lambda = 1.000000
> rc = 5.768340
> energy = -0.508438
> kinetic = 1.446182
> potential(screened) = -1.954620
> potential(ionic) = -6.573372
>
> izeta = 2
> rmatch = 3.964470
> splitnorm = 0.150000
> energy = -0.369093
> kinetic = 2.114234
> potential(screened) = -2.483327
> potential(ionic) = -7.516062
>
> POLgen: Perturbative polarization orbital with L= 2
>
> POLgen: Polarization orbital for state 3p
>
> izeta = 1
> rc = 5.768340
> energy = 0.654738
> kinetic = 2.018095
> potential(screened) = -1.363356
> potential(ionic) = -5.504727
> atom: Total number of Sankey-type orbitals: 13
>
> atm_pop: Valence configuration(local Pseudopot. screening):
> 3s( 2.00)
> 3p( 4.00)
> Vna: chval, zval: 6.00000 6.00000
>
> Vna: Cut-off radius for the neutral-atom potential: 5.768340
>
> atom:
> _________________________________________________________________________
>
> <basis_specs>
>
> ===============================================================================
> Au Z= 79 Mass= 196.97 Charge= 0.0000
> Lmxo=0 Lmxkb=1 BasisType=split Semic=F
> L=0 Nsemic=0 Cnfigmx=6
> n=1 nzeta=1 polorb=0
> vcte: 0.0000
> rinn: 0.0000
> rcs: 6.0000
> lambdas: 1.0000
>
> -------------------------------------------------------------------------------
> L=0 Nkbl=1 erefs: 0.17977+309
> L=1 Nkbl=1 erefs: 0.17977+309
>
> ===============================================================================
> </basis_specs>
>
> atom: Called for Au (Z = 79)
>
> read_vps: Pseudopotential generation method:
> read_vps: ATM 3.2.2 Troullier-Martins
>
> read_vps: Valence configuration (pseudopotential and basis set generation):
> 6s( 1.00) rc: 2.63
> 6p( 0.00) rc: 2.77
> Total valence charge: 1.00000
>
> atom: Pseudopotential generated from an ionic configuration
> atom: with net charge10.00
>
> xc_check: Exchange-correlation functional:
> xc_check: GGA Perdew, Burke & Ernzerhof 1996
> V l=0 = -2*Zval/r beyond r= 2.5678
> V l=1 = -2*Zval/r beyond r= 2.6994
> All V_l potentials equal beyond r= 2.6659
> This should be close to max(r_c) in ps generation
> All pots = -2*Zval/r beyond r= 2.6994
>
> VLOCAL1: 99.0% of the norm of Vloc inside 6.108 Ry
> VLOCAL1: 99.9% of the norm of Vloc inside 13.920 Ry
> atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.21569
> atom: Maximum radius for r*vlocal+2*Zval: 2.83783
> GHOST: No ghost state for L = 0
> GHOST: No ghost state for L = 1
>
> KBgen: Kleinman-Bylander projectors:
> l= 0 rc= 2.837834 el= -9.517724 Ekb= 5.458551 kbcos= 0.698235
> l= 1 rc= 2.873530 el= -7.976359 Ekb= 4.007714 kbcos= 0.708037
>
> KBgen: Total number of Kleinman-Bylander projectors: 4
> atom:
> -------------------------------------------------------------------------
>
> atom: SANKEY-TYPE ORBITALS:
>
> atom: basis set generated from the ionic configuration used
> atom: to generate the pseudopotential
>
> SPLIT: Orbitals with angular momentum L= 0
>
> SPLIT: Basis orbitals for state 6s
>
> izeta = 1
> lambda = 1.000000
> rc = 6.083298
> energy = -9.517804
> kinetic = 0.907700
> potential(screened) = -10.425504
> potential(ionic) = -10.902679
> atom: Total number of Sankey-type orbitals: 1
>
> atm_pop: Valence configuration(local Pseudopot. screening):
> 6s( 1.00)
> Vna: chval, zval: 1.00000 11.00000
>
> Vna: Cut-off radius for the neutral-atom potential: 6.083298
>
> atom:
> _________________________________________________________________________
>
> prinput: Basis input
> ----------------------------------------------------------
>
> PAO.BasisType split
>
> %block ChemicalSpeciesLabel
> 1 1 H # Species index, atomic number, species
> label
> 2 6 C # Species index, atomic number, species
> label
> 3 16 S # Species index, atomic number, species
> label
> 4 79 Au # Species index, atomic number, species
> label
> %endblock ChemicalSpeciesLabel
>
> %block PAO.Basis # Define Basis set
> H 1 # Species label, number of l-shells
> n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> 5.471 3.953
> 1.000 1.000
> C 2 # Species label, number of l-shells
> n=2 0 2 # n, l, Nzeta
> 4.633 3.432
> 1.000 1.000
> n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> 5.659 3.653
> 1.000 1.000
> S 2 # Species label, number of l-shells
> n=3 0 2 # n, l, Nzeta
> 4.606 3.543
> 1.000 1.000
> n=3 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
> 5.768 3.964
> 1.000 1.000
> Au 1 10.000 # Label, l-shells, ionic net charge
> n=6 0 1 # n, l, Nzeta
> 6.083
> 1.000
> %endblock PAO.Basis
>
> prinput:
> ----------------------------------------------------------------------
>
>
> siesta: ******************** Simulation parameters
> ****************************
> siesta:
> siesta: The following are some of the parameters of the simulation.
> siesta: A complete list of the parameters used, including defect values,
> siesta: can be found in file out.fdf
> siesta:
> coor: Atomic-coordinates input format = Cartesian coordinates
> coor: (in Angstroms)
> redata: Number of spin components = 1
> redata: Long output = F
> redata: Number of Atomic Species = 4
> redata: Charge density info will appear in .RHO file
> redata: Write Mulliken Pop. = Atomic and Orbital charges
> redata: Mesh Cutoff = 180.0000 Ry
> redata: Net charge of the system = 0.0000 |e|
> redata: Max. number of SCF Iter = 500
> redata: One Pulay mixing every = 5 iterations
> redata: Mix DM in first SCF step ? = F
> redata: Write Pulay info on disk? = F
> redata: New DM Mixing Weight = 0.1000
> redata: No kicks to SCF
> redata: DM Mixing Weight for Kicks = 0.5000
> redata: DM Tolerance for SCF = 0.000100
> redata: Use continuation files for DM = F
> redata: Neglect nonoverlap interactions = T
> redata: Method of Calculation = Diagonalization
> redata: Divide and Conquer = F
> redata: Electronic Temperature = 0.0019 Ry
> redata: Fix the spin of the system = F
> redata: Dynamics option = Verlet MD run
> redata: Initial MD time step = 1
> redata: Final MD time step = 1
> redata: Length of MD time step = 1.0000 fs
> redata: Length of MD time step = 1.0000 fs
> redata: Initial Temperature of MD run = 0.0000 K
> redata: Perform a MD quench = F
> redata:
> ***********************************************************************
>
> siesta: Atomic coordinates (Bohr) and species
> siesta: 0.00000 0.00000 0.00000 4 1
> siesta: 0.00000 7.70744 0.00000 4 2
> siesta: 3.85372 3.85372 0.00000 4 3
> siesta: 3.85372 11.56116 0.00000 4 4
> siesta: 7.70744 0.00000 0.00000 4 5
> siesta: 7.70744 7.70744 0.00000 4 6
> siesta: 11.56116 3.85372 0.00000 4 7
> siesta: 11.56116 11.56116 0.00000 4 8
> siesta: 0.00000 3.85372 3.85372 4 9
> siesta: 0.00000 11.56116 3.85372 4 10
> siesta: 3.85372 0.00000 3.85372 4 11
> siesta: 3.85372 7.70744 3.85372 4 12
> siesta: 7.70744 3.85372 3.85372 4 13
> siesta: 7.70744 11.56116 3.85372 4 14
> siesta: 11.56116 0.00000 3.85372 4 15
> siesta: 11.56116 7.70744 3.85372 4 16
> siesta: 0.00000 0.00000 7.70744 4 17
> siesta: 0.00000 7.70744 7.70744 4 18
> siesta: 3.85372 3.85372 7.70744 4 19
> siesta: 3.85372 11.56116 7.70744 4 20
> siesta: 7.70744 0.00000 7.70744 4 21
> siesta: 7.70744 7.70744 7.70744 4 22
> siesta: 11.56116 3.85372 7.70744 4 23
> siesta: 11.56116 11.56116 7.70744 4 24
> siesta: 0.00000 3.85372 11.56116 4 25
> siesta: 0.00000 11.56116 11.56116 4 26
> siesta: 3.85372 0.00000 11.56116 4 27
> siesta: 3.85372 7.70744 11.56116 4 28
> siesta: 7.70744 3.85372 11.56116 4 29
> siesta: 7.70744 11.56116 11.56116 4 30
> siesta: 11.56116 0.00000 11.56116 4 31
> siesta: 11.56116 7.70744 11.56116 4 32
> siesta: 0.00000 0.00000 15.41488 4 33
> siesta: 0.00000 7.70744 15.41488 4 34
> siesta: 3.85372 3.85372 15.41488 4 35
> siesta: 3.85372 11.56116 15.41488 4 36
> siesta: 7.70744 0.00000 15.41488 4 37
> siesta: 7.70744 7.70744 15.41488 4 38
> siesta: 11.56116 3.85372 15.41488 4 39
> siesta: 11.56116 11.56116 15.41488 4 40
> siesta: -0.12472 0.05291 19.26860 3 41
> siesta: 0.12094 -2.83270 24.17811 3 42
> siesta: -0.04913 0.08693 22.54728 2 43
> siesta: -0.13606 2.13539 24.22724 2 44
> siesta: -0.06992 1.33037 26.78915 2 45
> siesta: 0.06803 -1.32470 27.12419 2 46
> siesta: 0.13417 -2.13161 29.69082 2 47
> siesta: 0.04724 -0.07937 31.37419 2 48
> siesta: -0.12283 2.84026 29.74147 3 49
> siesta: 0.24377 -4.14795 30.28760 1 50
> siesta: -0.24566 4.15551 23.63765 1 51
> siesta: 0.12283 -0.04346 34.65476 3 52
> siesta: 0.00000 0.00000 38.50848 4 53
> siesta: 0.00000 7.70744 38.50848 4 54
> siesta: 3.85372 3.85372 38.50848 4 55
> siesta: 3.85372 11.56116 38.50848 4 56
> siesta: 7.70744 0.00000 38.50848 4 57
> siesta: 7.70744 7.70744 38.50848 4 58
> siesta: 11.56116 3.85372 38.50848 4 59
> siesta: 11.56116 11.56116 38.50848 4 60
> siesta: 0.00000 3.85372 42.36220 4 61
> siesta: 0.00000 11.56116 42.36220 4 62
> siesta: 3.85372 0.00000 42.36220 4 63
> siesta: 3.85372 7.70744 42.36220 4 64
> siesta: 7.70744 3.85372 42.36220 4 65
> siesta: 7.70744 11.56116 42.36220 4 66
> siesta: 11.56116 0.00000 42.36220 4 67
> siesta: 11.56116 7.70744 42.36220 4 68
> siesta: 0.00000 0.00000 46.21592 4 69
> siesta: 0.00000 7.70744 46.21592 4 70
> siesta: 3.85372 3.85372 46.21592 4 71
> siesta: 3.85372 11.56116 46.21592 4 72
> siesta: 7.70744 0.00000 46.21592 4 73
> siesta: 7.70744 7.70744 46.21592 4 74
> siesta: 11.56116 3.85372 46.21592 4 75
> siesta: 11.56116 11.56116 46.21592 4 76
> siesta: 0.00000 3.85372 50.06964 4 77
> siesta: 0.00000 11.56116 50.06964 4 78
> siesta: 3.85372 0.00000 50.06964 4 79
> siesta: 3.85372 7.70744 50.06964 4 80
> siesta: 7.70744 3.85372 50.06964 4 81
> siesta: 7.70744 11.56116 50.06964 4 82
> siesta: 11.56116 0.00000 50.06964 4 83
> siesta: 11.56116 7.70744 50.06964 4 84
> siesta: 0.00000 0.00000 53.92336 4 85
> siesta: 0.00000 7.70744 53.92336 4 86
> siesta: 3.85372 3.85372 53.92336 4 87
> siesta: 3.85372 11.56116 53.92336 4 88
> siesta: 7.70744 0.00000 53.92336 4 89
> siesta: 7.70744 7.70744 53.92336 4 90
> siesta: 11.56116 3.85372 53.92336 4 91
> siesta: 11.56116 11.56116 53.92336 4 92
>
> initatomlists: Number of atoms, orbitals, and projectors: 92 220
> 498
>
> siesta: System type = bulk
>
> * Maximum dynamic memory allocated = 3 MB
>
> siesta: ===============================
> SMEAGOL Bias step = 0, V = 0.000 Ry
> Begin CG move = 0
> ===============================
>
> InitMesh: MESH = 72 x 72 x 250 = 1296000
> InitMesh: Mesh cutoff (required, used) = 180.000 184.786 Ry
>
> * Maximum dynamic memory allocated = 128 MB
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> ------------------------------
>
> _______________________________________________
> Smeagol-discuss mailing list
> Smeagol-discuss at lists.tchpc.tcd.ie
> http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
>
> End of Smeagol-discuss Digest, Vol 18, Issue 4
> **********************************************
>
--
Assa Aravindh.S
Research Scholar
Theory and Computational Studies Section,
Material Science Division, IGCAR, India
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