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transiesta计算运行出错已有3人参与
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算的网上的例子，用并行计算的，散射区计算，出现 wrong solution method的错误，log文件如下： Siesta Version: siesta-3.0-rc2 Architecture : ifort-mkl-openmpi Compiler flags: mpif90 -O2 -xHost PARALLEL version * Running on 12 nodes in parallel >> Start of run: 16-MAY-2011 19:45:05 *********************** * WELCOME TO SIESTA * *********************** reinit: Reading from standard input ************************** Dump of input data file **************************** SystemName vacancy SystemLabel vacancy NumberOfAtoms 47 NumberOfSpecies 2 %block ChemicalSpeciesLabel 1 6 C 2 1 H %endblock ChemicalSpeciesLabel %block PAO.Basis # Define Basis set C 2 # Species label, number of l-shells n=2 0 1 # n, l, Nzeta 4.088 1.000 n=2 1 1 # n, l, Nzeta, Polarization, NzetaPol 4.870 1.000 H 1 n=1 0 1 4.500 1.000 %endblock PAO.Basis XC.functional GGA XC.authors PBE LatticeConstant 1.433600 Ang %block LatticeVectors 14.00000000 0.0000000000 0.0000000000 0.000000000 14.0000000000 0.0000000000 0.000000000 0.0000000000 10.3923048480 %endblock LatticeVectors AtomicCoordinatesFormat ScaledCartesian %block AtomicCoordinatesAndAtomicSpecies 0.0000000000 0.5000000000 0.8660254040 1 0.0000000000 -0.2500000000 0.8660254040 2 0.0000000000 1.0000000000 0.0000000000 1 0.0000000000 2.0000000000 0.0000000000 1 0.0000000000 0.5000000000 2.5980762120 1 0.0000000000 -0.2500000000 2.5980762120 2 0.0000000000 1.0000000000 1.7320508080 1 0.0000000000 2.0000000000 1.7320508080 1 0.0000000000 3.5000000000 0.8660254040 1 0.0000000000 2.5000000000 0.8660254040 1 0.0000000000 4.0000000000 0.0000000000 1 0.0000000000 4.7500000000 0.0000000000 2 0.0000000000 3.5000000000 2.5980762120 1 0.0000000000 2.5000000000 2.5980762120 1 0.0000000000 4.0000000000 1.7320508080 1 0.0000000000 4.7500000000 1.7320508080 2 0.0000000000 0.5000000000 4.3301270200 1 0.0000000000 -0.2500000000 4.3301270200 2 0.0000000000 1.0000000000 3.4641016160 1 0.0000000000 2.0000000000 3.4641016160 1 0.0000000000 0.5000000000 6.0621778280 1 0.0000000000 -0.2500000000 6.0621778280 2 0.0000000000 1.0000000000 5.1961524240 1 0.0000000000 2.0000000000 5.1961524240 1 0.0000000000 3.5000000000 4.3301270200 1 0.0000000000 4.0000000000 3.4641016160 1 0.0000000000 4.7500000000 3.4641016160 2 0.0000000000 3.5000000000 6.0621778280 1 0.0000000000 2.5000000000 6.0621778280 1 0.0000000000 4.0000000000 5.1961524240 1 0.0000000000 4.7500000000 5.1961524240 2 0.0000000000 0.5000000000 7.7942286360 1 0.0000000000 -0.2500000000 7.7942286360 2 0.0000000000 1.0000000000 6.9282032320 1 0.0000000000 2.0000000000 6.9282032320 1 0.0000000000 0.5000000000 9.5262794440 1 0.0000000000 -0.2500000000 9.5262794440 2 0.0000000000 1.0000000000 8.6602540400 1 0.0000000000 2.0000000000 8.6602540400 1 0.0000000000 3.5000000000 7.7942286360 1 0.0000000000 2.5000000000 7.7942286360 1 0.0000000000 4.0000000000 6.9282032320 1 0.0000000000 4.7500000000 6.9282032320 2 0.0000000000 3.5000000000 9.5262794440 1 0.0000000000 2.5000000000 9.5262794440 1 0.0000000000 4.0000000000 8.6602540400 1 0.0000000000 4.7500000000 8.6602540400 2 %endblock AtomicCoordinatesAndAtomicSpecies %block kgrid_Monkhorst_Pack 1 0 0 0.0 0 1 0 0.0 0 0 10 0.5 %endblock Kgrid_Monkhorst_Pack MeshCutoff 100.0 Ry MaxSCFIterations 500 DM.MixingWeight 0.1 DM.NumberPulay 5 DM.Tolerance 1.d-4 WriteCoorXmol .true. SolutionMethod transiesta TS.WriteHS .true. TS.NumUsedAtomsLeft 16 TS.NumUsedAtomsRight 16 TS.HSFileLeft '../electrode/nanoribbon.TSHS' TS.HSFileRight '../electrode/nanoribbon.TSHS' TS.TBT.HSFile './vacancy.TSHS' TS.TBT.Emin -4.0 eV TS.TBT.Emax 4.0 eV TS.TBT.NPoints 200 ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: vacancy reinit: ----------------------------------------------------------------------- reinit: System Label: vacancy reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Label: C Atomic number: 6 Species number: 2 Label: H Atomic number: 1 Ground state valence configuration: 2s02 2p02 Reading pseudopotential information in formatted form from C.psf Valence configuration for pseudopotential generation: 2s( 2.00) rc: 1.25 2p( 2.00) rc: 1.25 3d( 0.00) rc: 1.25 4f( 0.00) rc: 1.25 Ground state valence configuration: 1s01 Reading pseudopotential information in formatted form from H.psf Valence configuration for pseudopotential generation: 1s( 1.00) rc: 1.25 2p( 0.00) rc: 1.25 3d( 0.00) rc: 1.25 4f( 0.00) rc: 1.25 For C, 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 H, 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. =============================================================================== C Z= 6 Mass= 12.010 Charge= 0.17977+309 Lmxo=1 Lmxkb=2 BasisType=split Semic=F L=0 Nsemic=0 Cnfigmx=2 n=1 nzeta=1 polorb=0 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 4.0880 lambdas: 1.0000 L=1 Nsemic=0 Cnfigmx=2 n=1 nzeta=1 polorb=0 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 4.8700 lambdas: 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 =============================================================================== atom: Called for C (Z = 6) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins Total valence charge: 4.00000 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: GGA Perdew, Burke & Ernzerhof 1996 V l=0 = -2*Zval/r beyond r= 1.3270 V l=1 = -2*Zval/r beyond r= 1.3270 V l=2 = -2*Zval/r beyond r= 1.3270 All V_l potentials equal beyond r= 1.2311 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 1.3270 VLOCAL1: 99.0% of the norm of Vloc inside 28.641 Ry VLOCAL1: 99.9% of the norm of Vloc inside 65.273 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.48507 atom: Maximum radius for r*vlocal+2*Zval: 1.27815 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= 1.466618 el= -1.009804 Ekb= 7.916662 kbcos= 0.281323 l= 1 rc= 1.485071 el= -0.388706 Ekb= -4.690769 kbcos= -0.279005 l= 2 rc= 1.641300 el= 0.001971 Ekb= -1.223675 kbcos= -0.004991 KBgen: Total number of Kleinman-Bylander projectors: 9 atom: ------------------------------------------------------------------------- atom: SANKEY-TYPE ORBITALS: SPLIT: Orbitals with angular momentum L= 0 SPLIT: Basis orbitals for state 2s izeta = 1 lambda = 1.000000 rc = 4.088342 energy = -0.989113 kinetic = 0.943943 potential(screened) = -1.933056 potential(ionic) = -5.533072 SPLIT: Orbitals with angular momentum L= 1 SPLIT: Basis orbitals for state 2p izeta = 1 lambda = 1.000000 rc = 4.870301 energy = -0.368902 kinetic = 2.591513 potential(screened) = -2.960416 potential(ionic) = -6.456646 atom: Total number of Sankey-type orbitals: 4 atm_pop: Valence configuration (for 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: 4.870301 comcore: Pseudo-core radius Rcore= 1.791422 atom: _________________________________________________________________________ =============================================================================== H Z= 1 Mass= 1.0100 Charge= 0.17977+309 Lmxo=0 Lmxkb=1 BasisType=split Semic=F L=0 Nsemic=0 Cnfigmx=1 n=1 nzeta=1 polorb=0 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 4.5000 lambdas: 1.0000 ------------------------------------------------------------------------------- L=0 Nkbl=1 erefs: 0.17977+309 L=1 Nkbl=1 erefs: 0.17977+309 =============================================================================== atom: Called for H (Z = 1) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins 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= 1.2343 V l=1 = -2*Zval/r beyond r= 1.2189 All V_l potentials equal beyond r= 1.2343 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 1.2343 VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 atom: Maximum radius for r*vlocal+2*Zval: 1.21892 GHOST: No ghost state for L = 0 GHOST: No ghost state for L = 1 KBgen: Kleinman-Bylander projectors: l= 0 rc= 1.364359 el= -0.477200 Ekb= -2.021939 kbcos= -0.344793 l= 1 rc= 1.434438 el= 0.001076 Ekb= -0.443447 kbcos= -0.022843 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 1s izeta = 1 lambda = 1.000000 rc = 4.479210 energy = -0.451136 kinetic = 1.010721 potential(screened) = -1.461857 potential(ionic) = -1.992374 atom: Total number of Sankey-type orbitals: 1 atm_pop: Valence configuration (for local Pseudopot. screening): 1s( 1.00) Vna: chval, zval: 1.00000 1.00000 Vna: Cut-off radius for the neutral-atom potential: 4.479210 atom: _________________________________________________________________________ prinput: Basis input ---------------------------------------------------------- PAO.BasisType split %block ChemicalSpeciesLabel 1 6 C # Species index, atomic number, species label 2 1 H # Species index, atomic number, species label %endblock ChemicalSpeciesLabel %block PAO.Basis # Define Basis set C 2 # Species label, number of l-shells n=2 0 1 # n, l, Nzeta 4.088 1.000 n=2 1 1 # n, l, Nzeta 4.870 1.000 H 1 # Species label, number of l-shells n=1 0 1 # n, l, Nzeta 4.479 1.000 %endblock PAO.Basis prinput: ---------------------------------------------------------------------- coor: Atomic-coordinates input format = Cartesian coordinates coor: (in units of alat) siesta: Atomic coordinates (Bohr) and species siesta: 0.00000 1.35456 2.34616 1 1 siesta: 0.00000 -0.67728 2.34616 2 2 siesta: 0.00000 2.70911 0.00000 1 3 siesta: 0.00000 5.41822 0.00000 1 4 siesta: 0.00000 1.35456 7.03848 1 5 siesta: 0.00000 -0.67728 7.03848 2 6 siesta: 0.00000 2.70911 4.69232 1 7 siesta: 0.00000 5.41822 4.69232 1 8 siesta: 0.00000 9.48189 2.34616 1 9 siesta: 0.00000 6.77278 2.34616 1 10 siesta: 0.00000 10.83645 0.00000 1 11 siesta: 0.00000 12.86828 0.00000 2 12 siesta: 0.00000 9.48189 7.03848 1 13 siesta: 0.00000 6.77278 7.03848 1 14 siesta: 0.00000 10.83645 4.69232 1 15 siesta: 0.00000 12.86828 4.69232 2 16 siesta: 0.00000 1.35456 11.73080 1 17 siesta: 0.00000 -0.67728 11.73080 2 18 siesta: 0.00000 2.70911 9.38464 1 19 siesta: 0.00000 5.41822 9.38464 1 20 siesta: 0.00000 1.35456 16.42312 1 21 siesta: 0.00000 -0.67728 16.42312 2 22 siesta: 0.00000 2.70911 14.07696 1 23 siesta: 0.00000 5.41822 14.07696 1 24 siesta: 0.00000 9.48189 11.73080 1 25 siesta: 0.00000 10.83645 9.38464 1 26 siesta: 0.00000 12.86828 9.38464 2 27 siesta: 0.00000 9.48189 16.42312 1 28 siesta: 0.00000 6.77278 16.42312 1 29 siesta: 0.00000 10.83645 14.07696 1 30 siesta: 0.00000 12.86828 14.07696 2 31 siesta: 0.00000 1.35456 21.11544 1 32 siesta: 0.00000 -0.67728 21.11544 2 33 siesta: 0.00000 2.70911 18.76928 1 34 siesta: 0.00000 5.41822 18.76928 1 35 siesta: 0.00000 1.35456 25.80776 1 36 siesta: 0.00000 -0.67728 25.80776 2 37 siesta: 0.00000 2.70911 23.46160 1 38 siesta: 0.00000 5.41822 23.46160 1 39 siesta: 0.00000 9.48189 21.11544 1 40 siesta: 0.00000 6.77278 21.11544 1 41 siesta: 0.00000 10.83645 18.76928 1 42 siesta: 0.00000 12.86828 18.76928 2 43 siesta: 0.00000 9.48189 25.80776 1 44 siesta: 0.00000 6.77278 25.80776 1 45 siesta: 0.00000 10.83645 23.46160 1 46 siesta: 0.00000 12.86828 23.46160 2 47 siesta: System type = chain initatomlists: Number of atoms, orbitals, and projectors: 47 152 363 siesta: ******************** Simulation parameters **************************** siesta: siesta: The following are some of the parameters of the simulation. siesta: A complete list of the parameters used, including default values, siesta: can be found in file out.fdf siesta: redata: Non-Collinear-spin run = F redata: SpinPolarized (Up/Down) run = F redata: Number of spin components = 1 redata: Long output = F redata: Number of Atomic Species = 2 redata: Charge density info will appear in .RHO file redata: Write Mulliken Pop. = NO redata: Mesh Cutoff = 100.0000 Ry redata: Net charge of the system = 0.0000 |e| redata: Max. number of SCF Iter = 500 redata: Performing Pulay mixing using = 5 iterations redata: Mix DM in first SCF step ? = F redata: Write Pulay info on disk? = F redata: Discard 1st Pulay DM after kick = F redata: New DM Mixing Weight = 0.1000 redata: New DM Occupancy tolerance = 0.000000000001 redata: No kicks to SCF redata: DM Mixing Weight for Kicks = 0.5000 redata: DM Tolerance for SCF = 0.000100 redata: Require Energy convergence for SCF = F redata: DM Energy tolerance for SCF = 0.000100 eV redata: Require Harris convergence for SCF = F redata: DM Harris energy tolerance for SCF = 0.000100 eV redata: Using Saved Data (generic) = F redata: Use continuation files for DM = F redata: Neglect nonoverlap interactions = F redata: Method of Calculation = Transiesta 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: Initial Temperature of MD run = 0.0000 K redata: Perform a MD quench = F redata: *********************************************************************** ts_read_options: ************************************************************** ts_read_options: Save H and S matrices = T ts_read_options: Mixing Hamiltonian = F ts_read_options: TranSIESTA Voltage = 0.0000 Volts ts_read_options: TriDiag = F ts_read_options: Update DM Contact Reg. only = T ts_read_options: N. Buffer At. Left = 0 ts_read_options: N. Buffer At. Right = 0 ts_read_options: N. Pts. Circle = 24 ts_read_options: N. Pts. Line = 6 ts_read_options: N. Poles in Contour = 6 ts_read_options: N. Pts. Bias Contour = 5 ts_read_options: Contour E Min. = -3.0000 Ry ts_read_options: GFEta = 0.000001 Ry ts_read_options: Electronic Temperature = 0.0019 Ry ts_read_options: Bias Contour Method = gaussfermi ts_read_options: Left GF File = Left.GF ts_read_options: Right GF File = Right.GF ts_read_options: Calculate GF = T ts_read_options: Save S and quit (onlyS) = F ts_read_options: ************************************************************** ************************ Begin: TS CHECKS AND WARNINGS ************************ ************************ End: TS CHECKS AND WARNINGS ************************** Total number of electrons: 152.000000 Total ionic charge: 152.000000 * ProcessorY, Blocksize: 3 13 Kpoints in: 5 . Kpoints trimmed: 5 siesta: k-grid: Number of k-points = 5 siesta: k-grid: Cutoff (effective) = 10.035 Ang siesta: k-grid: Supercell and displacements siesta: k-grid: 1 0 0 0.000 siesta: k-grid: 0 1 0 0.000 siesta: k-grid: 0 0 10 0.500 Kpoints in: 1 . Kpoints trimmed: 1 transiesta: ts_k-grid: Number of Transport k-points = 1 transiesta: ts_k-grid: Supercell and displacements transiesta: ts_k-grid: 1 0 0 0.000 transiesta: ts_k-grid: 0 1 0 0.000 Naive supercell factors: 1 1 1 * Maximum dynamic memory allocated = 2 MB siesta: ============================== Begin MD step = 1 ============================== outcell: Unit cell vectors (Ang): 20.070400 0.000000 0.000000 0.000000 20.070400 0.000000 0.000000 0.000000 14.898408 outcell: Cell vector modules (Ang) : 20.070400 20.070400 14.898408 outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 outcell: Cell volume (Ang**3) : 6001.3910 New_DM. Step: 1 Initializing Density Matrix... InitMesh: MESH = 128 x 128 x 90 = 1474560 InitMesh: Mesh cutoff (required, used) = 100.000 100.857 Ry * Maximum dynamic memory allocated = 12 MB siesta: ERROR: wrong solution method siesta: ERROR: wrong solution method siesta: ERROR: wrong solution method siesta: ERROR: wrong solution method ERROR STOP from Node: 10 siesta: ERROR: wrong solution method ERROR STOP from Node: 1 siesta: ERROR: wrong solution method ERROR STOP from Node: 2 siesta: ERROR: wrong solution method ERROR STOP from Node: 3 ERROR STOP from Node: 0 ERROR STOP from Node: 4 siesta: ERROR: wrong solution method ERROR STOP from Node: 6 siesta: ERROR: wrong solution method ERROR STOP from Node: 7 siesta: ERROR: wrong solution method ERROR STOP from Node: 8 siesta: ERROR: wrong solution method ERROR STOP from Node: 9 ERROR STOP from Node: 5 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- siesta: ERROR: wrong solution method ERROR STOP from Node: 0 siesta: ERROR: wrong solution method ERROR STOP from Node: 1 siesta: ERROR: wrong solution method ERROR STOP from Node: 3 siesta: ERROR: wrong solution method ERROR STOP from Node: 4 siesta: ERROR: wrong solution method ERROR STOP from Node: 5 siesta: ERROR: wrong solution method ERROR STOP from Node: 9 siesta: ERROR: wrong solution method ERROR STOP from Node: 10 siesta: ERROR: wrong solution method ERROR STOP from Node: 2 siesta: ERROR: wrong solution method ERROR STOP from Node: 6 siesta: ERROR: wrong solution method ERROR STOP from Node: 7 siesta: ERROR: wrong solution method ERROR STOP from Node: 8 siesta: ERROR: wrong solution method ERROR STOP from Node: 11 siesta: ERROR: wrong solution method ERROR STOP from Node: 11 -------------------------------------------------------------------------- mpirun has exited due to process rank 5 with PID 4240 on node node8 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- [node8:04234] 11 more processes have sent help message help-mpi-api.txt / mpi-abort [node8:04234] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages |
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