[Smeagol-discuss] question for segmentation fault
김명자
mjkim9799 at gmail.com
Thu Jun 4 21:16:30 IST 2009
Dear folks
Does anyone have an idea about this error or this kind of error?
The output file is attached and input file is below.
It happened just at the start of MD step.
The lead calculation seemed to be done well.
Thank you,
Joonho
[joonho at gauss test]$ smeagol <dt1_tr.fdf > out
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
[joonho at gauss test]$ more dt1_tr.fdf
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
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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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