[Smeagol-discuss] for error in test file
Ivan Rungger
runggeri at tcd.ie
Tue Apr 21 10:49:38 IST 2009
Hello Joohno,
> I wonder if it is dependent on a version of siesta 1.3 and 1.3f1p.
This might indeed be the case. The code crashes inside siesta, so it
might be that with the older 1.3 version it does not work, in have not
tested it with siesta-1.3. Generally I suggest to use 1.3f1p. If it
still does not work for siesta-1.3f1p it is a compilation problem.
Cheers,
Ivan
>
> I hope you can catch the fault.
>
> Thank you,
>
> Joonho
>
>
> ------------------------------------------------------------------------
>
> [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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> Smeagol-discuss at lists.tchpc.tcd.ie
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--
=================================================
Ivan Rungger,
School of Physics and CRANN,
Trinity College Dublin,
Dublin 2, IRELAND
Phone: +353-1-8968454
Email: runggeri at tcd.ie
=================================================
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