[Smeagol-discuss] for error in test file
김명자
mjkim9799 at gmail.com
Mon Apr 20 18:06:21 IST 2009
Dear Ivan
I tested your file and attach the output because it is long.
I wonder if it is dependent on a version of siesta 1.3 and 1.3f1p.
I hope you can catch the fault.
Thank you,
Joonho
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[joonho at gauss leads]$ pwd
/home/joonho/smeagol.1.0/smeagol_examples/Au_wire_4kp/leads
[joonho at gauss leads]$ smeagol < Auwire_leads.fdf
SIESTA 1.3 -- [Release] (30 Jul 2003)
Architecture : intel-mkl
Compiler flags:
SERIAL version
* Running in serial mode
>> Start of run: 20-APR-2009 13:27:57
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file ****************************
# Sample SMEAGOL input file
# Ivan Rungger, February 2008
SystemName Au wire # Descriptive name of the system
SystemLabel Au.leads # Short name for naming files
NumberOfAtoms 2
NumberOfSpecies 1 # Number of species
PAO.BasisType split # Type of basis ('nones', 'nonodes', 'split')
PAO.SplitNorm 0.15 # Amount of norm carried by the second zeta
%block ChemicalSpeciesLabel
1 79 Au
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
Au 1
n=6 0 1 P 0 E 20 4
5.5
%endblock PAO.Basis
%block PS.lmax
Au 1
%endblock PS.lmax
LatticeConstant 1.000 Ang
%block LatticeVectors
12.000 0.000 0.000 1
0.000 12.000 0.000 1
0.000 0.000 5.600 1
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1 Au 1
0.000 0.000 2.800 1 Au 2
%endblock AtomicCoordinatesAndAtomicSpecies
#kgrid_cutoff 10 Ang
%block kgrid_Monkhorst_Pack
2 0 0 0.0
0 2 0 0.0
0 0 30 0.0
%endblock kgrid_Monkhorst_Pack
xc.functional LDA # 'LDA', 'GGA'
xc.authors CA # 'CA'='PZ', 'PW92', 'PBE'
SpinPolarized T # 'T', 'F'
FixSpin F
#TotalSpin 0.0
NonCollinearSpin F # 'T', 'F'
MeshCutoff 200 Ry # Equivalent plane wave cutoff for the grid
MaxSCFIterations 10000
DM.MixingWeight 0.1
DM.NumberPulay 4 # Pulay convergency accelerator
DM.MixSCF1 F
MixHamiltonian F
DM.PulayOnFile F # Store in memory ('F') or in files ('T')
#DM.NumberKick 30
#DM.KickMixingWeight 0.1
DM.Tolerance 0.5E-5
NeglNonOverlapInt F # 'F'=do not neglect
SolutionMethod diagon
ElectronicTemperature 300 K # Default value
DM.UseSaveDM T
#MD.UseSaveXV T
#MD.UseSaveCG T
WriteForces T
WriteCoorXmol T # Write Atoms coordinates
SaveElectrostaticPotential T
#SaveHS T # Save the Hamiltonian and Overlap matrices
SaveRho T # Save the valence pseudocharge density
#SaveDeltaRho T
#WriteDenchar T # Write Denchar output
WriteMullikenPop 1 #write mulliken population of aromic and orbital charges
#ParallelOverK T
#MullikenInSCF T
#MD.TypeOfRun CG # Type of MD Run. 'CG'=conjugate gradients
#MD.NumCGsteps 50 # Number of conjugate gradient minimization
#MD.MaxCGDispl 0.2 Bohr # Maximum atomic displacement
#MD.MaxForceTol 0.04 eV/Ang # Force Tollerance
#MD.MaxStressTol 0.01 GPa # Stress Tollerance
#MD.VariableCell F # Unit cell relaxation
#MD.TargetPressure 0.1 GPa
#WriteMDXmol T # Write Coordinate for movie
#WriteMDhistory T # Molecular Dynamics Trajectory
#%block LocalDensityOfStates
# -15.00 15.00 eV
#%endblock LocalDensityOfStates
#:%block ProjectedDensityOfStates
# -20.00 10.00 0.200 500 eV
#%endblock ProjectedDensityOfStates
#-----
#smeagol
#-----
BulkTransport T
BulkLeads LR
InitTransport T
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Au wire
reinit: -----------------------------------------------------------------------
reinit: System Label: Au.leads
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Label: Au Atomic number: 79
Ground state valence configuration: 6s01 5d10
Reading pseudopotential information in formatted form from Au.psf
Semicore shell(s) with ** electrons included in the valence for
Au
relmxkb: Read Max KB Ang. Momentum= 1 for species Au
<basis_specs>
===============================================================================
Au Z= 79 Mass= 196.97 Charge= 0.0000
Lmxo=0 Lmxkb=1 BasisType=split Semic=T
L=0 Nsemic=0 Cnfigmx=6
n=1 nzeta=1 polorb=0
vcte: 20.000
rinn: 4.0000
rcs: 5.5000
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: ATM3 Troullier-Martins
read_vps: Pseudopotential generated from a relativistic atomic calculation
read_vps: There are spin-orbit pseudopotentials available
read_vps: Spin-orbit interaction is not included in this calculation
read_vps: Valence configuration (pseudopotential and basis set generation):
6s( 1.00) rc: 2.29
6p( 0.00) rc: 2.29
Total valence charge: 1.00000
read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction
comcore: Pseudo-core radius Rcore= 7.714087
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 6.3158
V l=1 = -2*Zval/r beyond r= 6.3158
All V_l potentials equal beyond r= 2.2661
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 6.3158
Using large-core scheme for Vlocal
atom: Estimated core radius 6.31575
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 6.72309
atom: Maximum radius for r*vlocal+2*Zval: 6.39520
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 2.352642 el= -0.445660 Ekb= 4.785126 kbcos= 0.279017
l= 1 rc= 2.352642 el= -0.065043 Ekb= 2.856109 kbcos= 0.217743
KBgen: Total number of Kleinman-Bylander projectors: 4
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 6s
izeta = 1
lambda = 1.000000
rc = 5.504393
energy = -0.392859
kinetic = 0.507951
potential(screened) = -0.900809
potential(ionic) = -0.802802
atom: Total number of Sankey-type orbitals: 1
atm_pop: Valence configuration(local Pseudopot. screening):
6s( 1.00)
Vna: chval, zval: 1.00000 1.00000
Vna: Cut-off radius for the neutral-atom potential: 6.475639
Vna: WARNING: Cut-off radius for the neutral-atom potential, rVna = 6.47564
Vna: WARNING: Cut-off radius for charge density = 5.50439
Vna: WARNING: Check atom: Look for the sentence:
Vna: WARNING: LOCAL NEUTRAL-ATOM PSEUDOPOTENTIAL
Vna: WARNING: Increasing the tolerance parameter EPS
Vna: WARNING: might be a good idea
atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 79 Au # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
Au 1 # Species label, number of l-shells
n=6 0 1 # n, l, Nzeta
5.504
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 = 2
redata: Long output = F
redata: Number of Atomic Species = 1
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = Atomic and Orbital charges
redata: Mesh Cutoff = 200.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Max. number of SCF Iter = 10000
redata: One Pulay mixing every = 4 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 = 0.000005
redata: Antiferro initial spin density = F
redata: Use continuation files for DM = T
redata: Neglect nonoverlap interactions = F
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 1 1
siesta: 0.00000 0.00000 5.29124 1 2
initatomlists: Number of atoms, orbitals, and projectors: 2 2 8
siesta: System type = chain
siesta: k-grid: Number of k-points = 64
siesta: k-grid: Cutoff = 12.000 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 2 0 0 0.000
siesta: k-grid: 0 2 0 0.000
siesta: k-grid: 0 0 30 0.000
siesta: overlap: rmaxh veclen direction
siesta: overlap: 15.7141 22.6767 1
smeagol: The size of the cell is being expanded
smeagol: along the perpendicular direction to
smeagol: perform transport calculations
siesta: overlap: rmaxh veclen direction
siesta: overlap: 15.7141 22.6767 2
smeagol: The size of the cell is being expanded
smeagol: along the perpendicular direction to
smeagol: perform transport calculations
siesta: overlap: rmaxh veclen direction
siesta: overlap: 15.7141 10.5825 3
superc: Internal auxiliary supercell: 3 x 3 x 3 = 27
superc: Number of atoms, orbitals, and projectors: 54 54 216
* Maximum dynamic memory allocated = 1 MB
siesta: ===============================
Begin MD step = 1
===============================
superc: Internal auxiliary supercell: 3 x 3 x 3 = 27
superc: Number of atoms, orbitals, and projectors: 54 54 216
InitMesh: MESH = 108 x 108 x 48 = 559872
InitMesh: Mesh cutoff (required, used) = 200.000 203.052 Ry
* Maximum dynamic memory allocated = 39 MB
MKL ERROR : Parameter 1 was incorrect on entry to ZHEGV
cdiag: ERROR in routine zhegv:
1 -th argument had an illegal value
Terminating due to failed diagonalisation
Stopping Program
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