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overshiki新虫 (初入文坛)
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[求助]
siesta运行出现问题，Error in Cholesky factorisation in cdiag，原子间距过小，求助
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各位朋友，我学习siesta时间不是很长，今天遇到一个问题，我百思不得其解，有明白的大神，请多多指教。 问题是这样的： 出现错误信息 Error in Cholesky factorisation in cdiag 同时有warning siesta: WARNING: Atoms 1 319 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 2 102 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 3 281 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 4 64 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 5 51 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 6 14 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 7 278 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 8 61 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 10 281 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 11 64 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 12 290 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 13 73 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 15 23 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 16 287 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 17 70 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 19 290 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 20 73 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 21 299 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 22 82 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 24 32 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 25 296 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 26 79 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 28 299 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 29 82 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 30 308 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 31 91 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 33 41 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 34 305 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 35 88 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 37 308 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 38 91 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 39 317 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 40 100 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 42 50 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 43 314 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 44 97 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 46 317 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 47 100 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 48 319 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 49 102 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 52 323 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 53 106 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 55 102 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 56 156 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 57 64 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 58 118 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 59 105 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 60 68 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 62 115 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 65 118 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 66 73 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 67 127 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 69 77 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 71 124 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 74 127 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 75 82 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 76 136 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 78 86 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 80 133 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 83 136 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 84 91 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 85 145 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 87 95 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 89 142 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 92 145 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 93 100 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 94 154 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 96 104 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 98 151 too close: rij = 0.000000 Ang 数量相当多，有636个之多。 问题是我检查了原子间距，并没有问题。 下面是我的输入文件： SystemName Ag_electrode SystemLabel Ag_electrode NumberOfSpecies 1 NumberOfAtoms 9 %block ChemicalSpeciesLabel 1 47 Ag %endblock ChemicalSpeciesLabel PAO.EnergyShift 100 meV PAO.BasisType split PAO.BasisSize SZP AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies 0.000000 0.000000 0.203860 1 0.000000 1.000000 0.203860 1 1.000000 0.000000 0.203860 1 1.000000 1.000000 0.203860 1 0.000000 0.500000 0.097600 1 1.000000 0.500000 0.097600 1 0.500000 0.000000 0.097600 1 0.500000 1.000000 0.097600 1 0.500000 0.500000 0.203860 1 %endblock AtomicCoordinatesAndAtomicSpecies LatticeConstant 1 Ang %block LatticeParameters # Lattice vectors, in units of alat 4.267100 4.267100 17.623800 90 90 90 %endblock LatticeParameters #%block LatticeVectors 8.65128000 0.00000000 0.00000000 0.00000000 9.98964000 0.00000000 0.00000000 0.00000000 7.06374000 #%endblock LatticeVectors kgrid_cutoff 5 Ang #%block kgrid_Monkhorst_Pack 4 0 0 0.5 0 4 0 0.5 0 0 6 0.5 #%endblock kgrid_Monkhorst_Pack # SPIN options xc.functional LDA # Exchange-correlation functional xc.authors CA # Exchange-correlation version SpinPolarized F # Logical parameters are: yes or no FixSpin F TotalSpin 0.0 NonCollinearSpin F # 'T', 'F' MeshCutoff 20 Ry # Equivalent plane wave cutoff for the grid # SCF options DM.Tolerance 1.d-4 # Tolerance in maximum difference between input and output DM MaxSCFIterations 300 # Maximum number of SCF iter #DM.UseSaveDM T # to use continuation files DM.MixingWeight 0.25 # New DM amount for next SCF cycle DM.NumberPulay 0 DM.MixSCF1 F DM.PulayOnFile F # Store in memory ('F') or in files ('T') # NeglNonOverlapInt T # 'F'=do not neglect SolutionMethod Diagon # OrderN or Diagon or transiesta if you do a transport calculation #ElectronicTemperature 300 K # Temp. for Fermi smearing # MD options MD.TypeOfRun CG # Type of dynamics: MD.VariableCell F MD.NumCGsteps 100 # Number of CG steps for coordinate optimization #ZM.UnitsLength Ang #the units of length used during Z-matrix input #ZM.UnitsAngle deg #the units of angles used during Z-matrix input #ZM.ForceTolLength 0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths #ZM.ForceTolAngle 0.00356549 Ry/rad #controls the convergence with respect to forces on Z-matrix angles #ZM.MaxDisplLength 0.1 Ang # controls the maximum change in a Zmatrix length during an optimisation step #ZM.MaxDisplAngle 0.003 rad # controls the maximum change in a Z-matrix angle during an optimisation step #ZM.CalcAllForces T # Default value # Output options WriteCoorInitial T WriteCoorStep T WriteCoorXmol T WriteForces T WriteEigenvalues F # If .false., it writes them in the file Systemlabel.EIG WriteMullikenPop 1 # Write Mulliken Population Analysis #WriteKpoints T #WriteKbands T #WriteBands T WriteMDCoorXmol T WriteMDhistory T WriteSiestaDim T WriteDenchar T siesta的运行结果： ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: Ag_electrode reinit: ----------------------------------------------------------------------- reinit: System Label: Ag_electrode reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Label: Ag Atomic number: 47 Ground state valence configuration: 5s01 4d10 Reading pseudopotential information in formatted form from Ag.psf Valence configuration for pseudopotential generation: 5s( 1.00) rc: 2.49 5p( 0.00) rc: 2.72 4d(10.00) rc: 2.49 4f( 0.00) rc: 2.49 For Ag, 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. =============================================================================== Ag Z= 47 Mass= 107.87 Charge= 0.17977+309 Lmxo=2 Lmxkb= 3 BasisType=split Semic=F L=0 Nsemic=0 Cnfigmx=5 n=1 nzeta=1 polorb=1 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 0.0000 lambdas: 1.0000 L=1 Nsemic=0 Cnfigmx=5 L=2 Nsemic=0 Cnfigmx=4 n=1 nzeta=1 polorb=0 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 0.0000 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 L=3 Nkbl=1 erefs: 0.17977+309 =============================================================================== atom: Called for Ag (Z = 47) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins Total valence charge: 11.00000 xc_check: Exchange-correlation functional: xc_check: Ceperley-Alder V l=0 = -2*Zval/r beyond r= 3.7148 V l=1 = -2*Zval/r beyond r= 3.7148 V l=2 = -2*Zval/r beyond r= 3.7148 V l=3 = -2*Zval/r beyond r= 3.7148 All V_l potentials equal beyond r= 2.6507 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 3.7148 Using large-core scheme for Vlocal atom: Estimated core radius 3.71485 atom: Including non-local core corrections could be a good idea atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 4.05455 atom: Maximum radius for r*vlocal+2*Zval: 3.76158 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= 2.752015 el= -0.315347 Ekb= 2.959784 kbcos= 0.215922 l= 1 rc= 2.752015 el= -0.064585 Ekb= 1.174286 kbcos= 0.223992 l= 2 rc= 2.717828 el= -0.597077 Ekb= -8.608930 kbcos= -0.745607 l= 3 rc= 2.752015 el= 0.003478 Ekb= -2.784593 kbcos= -0.016304 KBgen: Total number of Kleinman-Bylander projectors: 16 atom: ------------------------------------------------------------------------- atom: SANKEY-TYPE ORBITALS: SPLIT: Orbitals with angular momentum L= 0 SPLIT: Basis orbitals for state 5s SPLIT: PAO cut-off radius determined from an SPLIT: energy shift= 0.007350 Ry izeta = 1 lambda = 1.000000 rc = 7.766702 energy = -0.308537 kinetic = 0.276782 potential(screened) = -0.585319 potential(ionic) = -7.642186 SPLIT: Orbitals with angular momentum L= 2 SPLIT: Basis orbitals for state 4d SPLIT: PAO cut-off radius determined from an SPLIT: energy shift= 0.007350 Ry izeta = 1 lambda = 1.000000 rc = 4.594413 energy = -0.590771 kinetic = 6.015485 potential(screened) = -6.606255 potential(ionic) = -18.502124 POLgen: Perturbative polarization orbital with L= 1 POLgen: Polarization orbital for state 5s izeta = 1 rc = 7.766702 energy = -0.042356 kinetic = 0.501615 potential(screened) = -0.543970 potential(ionic) = -7.056866 atom: Total number of Sankey-type orbitals: 9 atm_pop: Valence configuration (for local Pseudopot. screening): 5s( 1.00) 5p( 0.00) 4d(10.00) Vna: chval, zval: 11.00000 11.00000 Vna: Cut-off radius for the neutral-atom potential: 7.766702 atom: _________________________________________________________________________ prinput: Basis input ---------------------------------------------------------- PAO.BasisType split %block ChemicalSpeciesLabel 1 47 Ag # Species index, atomic number, species label %endblock ChemicalSpeciesLabel %block PAO.Basis # Define Basis set Ag 2 # Species label, number of l-shells n=5 0 1 P 1 # n, l, Nzeta, Polarization, NzetaPol 7.767 1.000 n=4 2 1 # n, l, Nzeta 4.594 1.000 %endblock PAO.Basis prinput: ---------------------------------------------------------------------- coor: Atomic-coordinates input format = Fractional siesta: Atomic coordinates (Bohr) and species siesta: 0.00000 0.00000 6.78939 1 1 siesta: 0.00000 8.06365 6.78939 1 2 siesta: 8.06365 0.00000 6.78939 1 3 siesta: 8.06365 8.06365 6.78939 1 4 siesta: 0.00000 4.03183 3.25049 1 5 siesta: 8.06365 4.03183 3.25049 1 6 siesta: 4.03183 0.00000 3.25049 1 7 siesta: 4.03183 8.06365 3.25049 1 8 siesta: 4.03183 4.03183 6.78939 1 9 siesta: System type = slab initatomlists: Number of atoms, orbitals, and projectors: 9 81 144 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 = 1 redata: Charge density info will appear in .RHO file redata: Write Mulliken Pop. = Atomic and Orbital charges redata: Mesh Cutoff = 20.0000 Ry redata: Net charge of the system = 0.0000 |e| redata: Max. number of SCF Iter = 300 redata: Mixing is linear 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 = 0.2500 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 = Diagonalization redata: Divide and Conquer = T redata: Electronic Temperature = 0.0019 Ry redata: Fix the spin of the system = F redata: Dynamics option = CG coord. optimization redata: Variable cell = F redata: Use continuation files for CG = F redata: Max atomic displ per move = 0.2000 Bohr redata: Maximum number of CG moves = 100 redata: Force tolerance = 0.0016 Ry/Bohr redata: *********************************************************************** Total number of electrons: 99.000000 Total ionic charge: 99.000000 Kpoints in: 6 . Kpoints trimmed: 5 siesta: k-grid: Number of k-points = 5 siesta: k-grid: Cutoff (effective) = 6.401 Ang siesta: k-grid: Supercell and displacements siesta: k-grid: 0 3 0 0.000 siesta: k-grid: 3 0 0 0.000 siesta: k-grid: 0 0 1 0.000 Naive supercell factors: 6 6 2 superc: Internal auxiliary supercell: 6 x 6 x 2 = 72 superc: Number of atoms, orbitals, and projectors: 648 5832 10368 * Maximum dynamic memory allocated = 1 MB siesta: ============================== Begin CG move = 0 ============================== outcoor: Atomic coordinates (fractional): 0.00000000 0.00000000 0.20386000 1 1 Ag 0.00000000 1.00000000 0.20386000 1 2 Ag 1.00000000 0.00000000 0.20386000 1 3 Ag 1.00000000 1.00000000 0.20386000 1 4 Ag 0.00000000 0.50000000 0.09760000 1 5 Ag 1.00000000 0.50000000 0.09760000 1 6 Ag 0.50000000 0.00000000 0.09760000 1 7 Ag 0.50000000 1.00000000 0.09760000 1 8 Ag 0.50000000 0.50000000 0.20386000 1 9 Ag superc: Internal auxiliary supercell: 6 x 6 x 2 = 72 superc: Number of atoms, orbitals, and projectors: 648 5832 10368 outcell: Unit cell vectors (Ang): 4.267100 0.000000 0.000000 0.000000 4.267100 0.000000 0.000000 0.000000 17.623800 outcell: Cell vector modules (Ang) : 4.267100 4.267100 17.623800 outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 outcell: Cell volume (Ang**3) : 320.8967 siesta: WARNING: Atoms 1 319 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 2 102 too close: rij = 0.000000 Ang siesta: WARNING: Atoms 3 281 too close: rij = 0.000000 Ang 。。。。。。。。。 New_DM. Step: 1 Initializing Density Matrix... InitMesh: MESH = 12 x 12 x 48 = 6912 InitMesh: Mesh cutoff (required, used) = 20.000 20.501 Ry * Maximum dynamic memory allocated = 11 MB Error in Cholesky factorisation in cdiag ERROR STOP from Node: 0 请多多指教，谢谢！ |
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overshiki
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yangxuezhang
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