Your MD.FClast Is ill defined, please see the manual for how to correctly set its value.
-- Kind regards Nick Papior On 24 Aug 2015 06:42, "Saeed Nasiri" <[email protected]> wrote: > Dear users > > I want to calculate vibration frequency for coronene molecule, so at first > an > optimization computation was run and then a FC computation, but the > coronene.FC file is empty. Could anyone help me??? > > best regards > Nasri > ========================== FDF ===================================== > SystemLabel coroneneFC > NumberOfAtoms 36 > NumberOfSpecies 2 > > %block ChemicalSpeciesLabel > 1 6 C > 2 1 H > %endblock ChemicalSpeciesLabel > > AtomicCoordinatesFormat NotScaledCartesianAng > %block AtomicCoordinatesAndAtomicSpecies > 1.255000000 3.558000000 0.000000000 1 > -0.000000000 2.864000000 0.000000000 1 > -0.000000000 1.435000000 0.000000000 1 > 1.243000000 0.718000000 0.000000000 1 > 2.480000000 1.432000000 0.000000000 1 > 2.454000000 2.866000000 0.000000000 1 > -1.243000000 0.718000000 0.000000000 1 > 1.243000000 -0.718000000 0.000000000 1 > -0.000000000 -1.435000000 0.000000000 1 > -1.243000000 -0.718000000 0.000000000 1 > -0.000000000 -2.864000000 0.000000000 1 > 1.255000000 -3.558000000 0.000000000 1 > 2.454000000 -2.866000000 0.000000000 1 > 2.480000000 -1.432000000 0.000000000 1 > 3.709000000 -0.692000000 0.000000000 1 > 3.709000000 0.692000000 0.000000000 1 > 4.648000000 1.240000000 0.000000000 2 > 4.648000000 -1.240000000 0.000000000 2 > 1.250000000 4.646000000 0.000000000 2 > 3.398000000 3.406000000 0.000000000 2 > 1.250000000 -4.646000000 0.000000000 2 > 3.398000000 -3.406000000 0.000000000 2 > -1.255000000 3.558000000 0.000000000 1 > -2.454000000 2.866000000 0.000000000 1 > -2.480000000 1.432000000 0.000000000 1 > -1.250000000 4.646000000 0.000000000 2 > -3.398000000 3.406000000 0.000000000 2 > -3.709000000 0.692000000 0.000000000 1 > -3.709000000 -0.692000000 0.000000000 1 > -2.480000000 -1.432000000 0.000000000 1 > -4.648000000 1.240000000 0.000000000 2 > -4.648000000 -1.240000000 0.000000000 2 > -1.255000000 -3.558000000 0.000000000 1 > -1.250000000 -4.646000000 0.000000000 2 > -2.454000000 -2.866000000 0.000000000 1 > -3.398000000 -3.406000000 0.000000000 2 > %endblock AtomicCoordinatesAndAtomicSpecies > > > PAO.BasisType split > PAO.BasisSize DZP > SolutionMethod diagon > PAO.SplitNorm 0.150000 > PAO.EnergyShift 0.020000 Ry > Harris_functional false > XC.functional LDA > XC.Authors PZ > SpinPolarized false > MeshCutoff 250.000000 Ry > ElectronicTemperature 300.000000 K > MaxSCFIterations 50 > DM.NumberPulay 0 > DM.MixingWeight 0.250000 > MD.TypeOfRun FC > MD.VariableCell false > MD.NumCGsteps 18831536 > MD.MaxCGDispl 0.200000 Bohr > MD.PreconditionVariableCell 5.000000 Ang > MD.MaxStressTol 1.000000 GPa > MD.UseSaveXV false > > %block MD.TargetStress > -1.000000 -1.000000 -1.000000 0.000000 0.000000 0.000000 > %endblock MD.TargetStress > > MD.MaxForceTol 0.040000 eV/Ang > MD.InitialTimeStep 1 > MD.FinalTimeStep 1 > MD.LengthTimeStep 1 fs > MD.InitialTemperature 0.000000 K > MD.Quench false > MD.TargetTemperature 0.000000 K > MD.NoseMass 100.000000 Ry*fs**2 > MD.ParrinelloRahmanMass 100.000000 Ry*fs**2 > MD.AnnealOption TemperatureandPressure > MD.TauRelax 100.000000 fs > MD.BulkModulus 100.000000 Ry/Bohr**3 > MD.TargetPressure 0.000000 GPa > MD.FCDispl 0.040000 Bohr > MD.FCfirst 1 > MD.FClast 0 > > UseSaveData true > WriteCoorInital true > WriteCoorStep false > WriteForces false > WriteKpoints true > WriteEigenvalues false > WriteKbands false > WriteBands false > WriteWaveFunctions false > WriteMullikenPop 0 > WriteDM true > WriteCoorXmol false > WriteCoorCerius true > WriteMDXmol false > WriteMDhistory true > > %block ProjectedDensityOfStates > -23.00 50.00 0.100 1000 eV > %endblock ProjectedDensityOfStates > > %block GridCellSampling > 0.5 0.5 0.5 > %endblock GridCellSampling > > writedensityofstate true > NumberOfEigenStates 1000 > > > ============================= out ======================================= > Siesta Version: siesta-3.2 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: f95 -g -O2 > SERIAL version > > * Running in serial mode > >> Start of run: 24-AUG-2015 8:36:57 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > # Created by GDIS version 0.90.0 > # > # *** should be changed *** > SystemLabel coroneneFC > NumberOfAtoms 36 > NumberOfSpecies 2 > %block ChemicalSpeciesLabel > 1 6 C > 2 1 H > %endblock ChemicalSpeciesLabel > AtomicCoordinatesFormat NotScaledCartesianAng > %block AtomicCoordinatesAndAtomicSpecies > 1.255000000 3.558000000 0.000000000 1 > -0.000000000 2.864000000 0.000000000 1 > -0.000000000 1.435000000 0.000000000 1 > 1.243000000 0.718000000 0.000000000 1 > 2.480000000 1.432000000 0.000000000 1 > 2.454000000 2.866000000 0.000000000 1 > -1.243000000 0.718000000 0.000000000 1 > 1.243000000 -0.718000000 0.000000000 1 > -0.000000000 -1.435000000 0.000000000 1 > -1.243000000 -0.718000000 0.000000000 1 > -0.000000000 -2.864000000 0.000000000 1 > 1.255000000 -3.558000000 0.000000000 1 > 2.454000000 -2.866000000 0.000000000 1 > 2.480000000 -1.432000000 0.000000000 1 > 3.709000000 -0.692000000 0.000000000 1 > 3.709000000 0.692000000 0.000000000 1 > 4.648000000 1.240000000 0.000000000 2 > 4.648000000 -1.240000000 0.000000000 2 > 1.250000000 4.646000000 0.000000000 2 > 3.398000000 3.406000000 0.000000000 2 > 1.250000000 -4.646000000 0.000000000 2 > 3.398000000 -3.406000000 0.000000000 2 > -1.255000000 3.558000000 0.000000000 1 > -2.454000000 2.866000000 0.000000000 1 > -2.480000000 1.432000000 0.000000000 1 > -1.250000000 4.646000000 0.000000000 2 > -3.398000000 3.406000000 0.000000000 2 > -3.709000000 0.692000000 0.000000000 1 > -3.709000000 -0.692000000 0.000000000 1 > -2.480000000 -1.432000000 0.000000000 1 > -4.648000000 1.240000000 0.000000000 2 > -4.648000000 -1.240000000 0.000000000 2 > -1.255000000 -3.558000000 0.000000000 1 > -1.250000000 -4.646000000 0.000000000 2 > -2.454000000 -2.866000000 0.000000000 1 > -3.398000000 -3.406000000 0.000000000 2 > %endblock AtomicCoordinatesAndAtomicSpecies > PAO.BasisType split > PAO.BasisSize DZP > SolutionMethod diagon > PAO.SplitNorm 0.150000 > PAO.EnergyShift 0.020000 Ry > Harris_functional false > XC.functional LDA > XC.Authors PZ > SpinPolarized false > MeshCutoff 250.000000 Ry > ElectronicTemperature 300.000000 K > MaxSCFIterations 50 > DM.NumberPulay 0 > DM.MixingWeight 0.250000 > MD.TypeOfRun FC > MD.VariableCell false > MD.NumCGsteps 18831536 > MD.MaxCGDispl 0.200000 Bohr > MD.PreconditionVariableCell 5.000000 Ang > MD.MaxStressTol 1.000000 GPa > MD.UseSaveXV false > %block MD.TargetStress > -1.000000 -1.000000 -1.000000 0.000000 0.000000 0.000000 > %endblock MD.TargetStress > MD.MaxForceTol 0.040000 eV/Ang > MD.InitialTimeStep 1 > MD.FinalTimeStep 1 > MD.LengthTimeStep 1 fs > MD.InitialTemperature 0.000000 K > MD.Quench false > MD.TargetTemperature 0.000000 K > MD.NoseMass 100.000000 Ry*fs**2 > MD.ParrinelloRahmanMass 100.000000 Ry*fs**2 > MD.AnnealOption TemperatureandPressure > MD.TauRelax 100.000000 fs > MD.BulkModulus 100.000000 Ry/Bohr**3 > MD.TargetPressure 0.000000 GPa > MD.FCDispl 0.040000 Bohr > MD.FCfirst 1 > MD.FClast 0 > UseSaveData true > WriteCoorInital true > WriteCoorStep false > WriteForces false > WriteKpoints true > WriteEigenvalues false > WriteKbands false > WriteBands false > WriteWaveFunctions false > WriteMullikenPop 0 > WriteDM true > WriteCoorXmol false > WriteCoorCerius true > WriteMDXmol false > WriteMDhistory true > %block ProjectedDensityOfStates > -23.00 50.00 0.100 1000 eV > %endblock ProjectedDensityOfStates > %block GridCellSampling > 0.5 0.5 0.5 > %endblock GridCellSampling > writedensityofstate true > NumberOfEigenStates 1000 > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: > reinit: > ----------------------------------------------------------------------- > reinit: System Label: coroneneFC > 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: 1.54 > 2p( 2.00) rc: 1.54 > 3d( 0.00) rc: 1.54 > 4f( 0.00) rc: 1.54 > Ground state valence configuration: 1s01 > Reading pseudopotential information in formatted form from H.psf > > Valence configuration for pseudopotential generation: > 1s( 1.00) rc: 1.31 > 2p( 0.00) rc: 1.31 > 3d( 0.00) rc: 0.37 > 4f( 0.00) rc: 1.31 > 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 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. > > <basis_specs> > > =============================================================================== > C Z= 6 Mass= 12.010 Charge= 0.17977+309 > Lmxo=1 Lmxkb= 3 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=2 > n=1 nzeta=2 polorb=0 > splnorm: 0.15000 > 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 > splnorm: 0.15000 > 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: ATM3 Troullier-Martins > Total valence charge: 4.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > 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= 1.5038 > All V_l potentials equal beyond r= 1.5227 > 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 18.722 Ry > VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.83678 > atom: Maximum radius for r*vlocal+2*Zval: 1.58088 > 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= 1.747182 el= -1.001948 Ekb= 4.950286 kbcos= 0.319819 > l= 1 rc= 1.747182 el= -0.398598 Ekb= -4.108613 kbcos= -0.367053 > l= 2 rc= 1.930978 el= 0.002326 Ekb= -1.042946 kbcos= -0.009366 > l= 3 rc= 2.055542 el= 0.003420 Ekb= -0.408633 kbcos= -0.001262 > > 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 determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.191849 > energy = -0.983897 > kinetic = 0.880927 > potential(screened) = -1.864824 > potential(ionic) = -5.475687 > > izeta = 2 > rmatch = 3.431921 > splitnorm = 0.150000 > energy = -0.853083 > kinetic = 1.298222 > potential(screened) = -2.151305 > potential(ionic) = -5.995890 > > SPLIT: Orbitals with angular momentum L= 1 > > SPLIT: Basis orbitals for state 2p > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.870301 > energy = -0.379093 > kinetic = 2.540023 > potential(screened) = -2.919116 > potential(ionic) = -6.427960 > > izeta = 2 > rmatch = 3.475094 > splitnorm = 0.150000 > energy = -0.215057 > kinetic = 3.814571 > potential(screened) = -4.029628 > potential(ionic) = -7.920250 > > POLgen: Perturbative polarization orbital with L= 2 > > POLgen: Polarization orbital for state 2p > > izeta = 1 > rc = 4.870301 > energy = 1.280996 > kinetic = 2.631310 > potential(screened) = -1.350314 > potential(ionic) = -4.295640 > atom: Total number of Sankey-type orbitals: 13 > > 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 > > atom: > _________________________________________________________________________ > > <basis_specs> > > =============================================================================== > H Z= 1 Mass= 1.0100 Charge= 0.17977+309 > Lmxo=0 Lmxkb= 2 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=1 > n=1 nzeta=2 polorb=1 > splnorm: 0.15000 > 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: ATM3 Troullier-Martins > Total valence charge: 1.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 1.2977 > V l=1 = -2*Zval/r beyond r= 1.2815 > V l=2 = -2*Zval/r beyond r= 1.1307 > All V_l potentials equal beyond r= 1.2977 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 1.2977 > > VLOCAL1: 99.0% of the norm of Vloc inside 25.776 Ry > VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.52711 > atom: Maximum radius for r*vlocal+2*Zval: 1.28155 > 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= 1.434438 el= -0.467325 Ekb= -1.940326 kbcos= -0.353040 > l= 1 rc= 1.508111 el= 0.001430 Ekb= -0.480826 kbcos= -0.024144 > l= 2 rc= 1.527112 el= 0.002365 Ekb= -0.479392 kbcos= -0.001656 > > 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 determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.828263 > energy = -0.449375 > kinetic = 0.925762 > potential(screened) = -1.375137 > potential(ionic) = -1.911235 > > izeta = 2 > rmatch = 3.854947 > splitnorm = 0.150000 > energy = -0.336149 > kinetic = 1.498089 > potential(screened) = -1.834238 > potential(ionic) = -2.406110 > > POLgen: Perturbative polarization orbital with L= 1 > > POLgen: Polarization orbital for state 1s > > izeta = 1 > rc = 4.828263 > energy = 0.707053 > kinetic = 1.398668 > potential(screened) = -0.691614 > potential(ionic) = -1.171973 > atom: Total number of Sankey-type orbitals: 5 > > 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: 4.828263 > > 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 2 # n, l, Nzeta > 4.192 3.432 > 1.000 1.000 > n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 4.870 3.475 > 1.000 1.000 > H 1 # Species label, number of > l-shells > n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol > 4.828 3.855 > 1.000 1.000 > %endblock PAO.Basis > > prinput: > ---------------------------------------------------------------------- > > coor: Atomic-coordinates input format = Cartesian coordinates > coor: (in Angstroms) > > siesta: Atomic coordinates (Bohr) and species > siesta: 2.37161 6.72365 0.00000 1 1 > siesta: -0.00000 5.41218 0.00000 1 2 > siesta: -0.00000 2.71176 0.00000 1 3 > siesta: 2.34893 1.35682 0.00000 1 4 > siesta: 4.68652 2.70609 0.00000 1 5 > siesta: 4.63739 5.41596 0.00000 1 6 > siesta: -2.34893 1.35682 0.00000 1 7 > siesta: 2.34893 -1.35682 0.00000 1 8 > siesta: -0.00000 -2.71176 0.00000 1 9 > siesta: -2.34893 -1.35682 0.00000 1 10 > siesta: -0.00000 -5.41218 0.00000 1 11 > siesta: 2.37161 -6.72365 0.00000 1 12 > siesta: 4.63739 -5.41596 0.00000 1 13 > siesta: 4.68652 -2.70609 0.00000 1 14 > siesta: 7.00900 -1.30769 0.00000 1 15 > siesta: 7.00900 1.30769 0.00000 1 16 > siesta: 8.78345 2.34326 0.00000 2 17 > siesta: 8.78345 -2.34326 0.00000 2 18 > siesta: 2.36216 8.77967 0.00000 2 19 > siesta: 6.42129 6.43641 0.00000 2 20 > siesta: 2.36216 -8.77967 0.00000 2 21 > siesta: 6.42129 -6.43641 0.00000 2 22 > siesta: -2.37161 6.72365 0.00000 1 23 > siesta: -4.63739 5.41596 0.00000 1 24 > siesta: -4.68652 2.70609 0.00000 1 25 > siesta: -2.36216 8.77967 0.00000 2 26 > siesta: -6.42129 6.43641 0.00000 2 27 > siesta: -7.00900 1.30769 0.00000 1 28 > siesta: -7.00900 -1.30769 0.00000 1 29 > siesta: -4.68652 -2.70609 0.00000 1 30 > siesta: -8.78345 2.34326 0.00000 2 31 > siesta: -8.78345 -2.34326 0.00000 2 32 > siesta: -2.37161 -6.72365 0.00000 1 33 > siesta: -2.36216 -8.77967 0.00000 2 34 > siesta: -4.63739 -5.41596 0.00000 1 35 > siesta: -6.42129 -6.43641 0.00000 2 36 > > siesta: Automatic unit cell vectors (Ang): > siesta: 15.846612 0.000000 0.000000 > siesta: 0.000000 15.842212 0.000000 > siesta: 0.000000 0.000000 5.669953 > > siesta: System type = molecule > > initatomlists: Number of atoms, orbitals, and projectors: 36 372 > 492 > > 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 = 250.0000 Ry > redata: Net charge of the system = 0.0000 |e| > redata: Max. number of SCF Iter = 50 > 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) = T > redata: Use continuation files for DM = T > 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 = Force Constants Matrix > Calculation > redata: Atomic displ for force constants = 0.0400 Bohr > redata: First atom to move = 1 > redata: Last atom to move = 0 > redata: > *********************************************************************** > Total number of electrons: 108.000000 > Total ionic charge: 108.000000 > Kpoints in: 1 . Kpoints trimmed: 1 > > siesta: k-point coordinates (Bohr**-1) and weights: > siesta: 1 0.000000 0.000000 0.000000 1.000000 > > siesta: k-grid: Number of k-points = 1 > siesta: k-grid: Cutoff (effective) = 2.835 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 1 0.000 > > * Maximum dynamic memory allocated = 2 MB > > siesta: ============================== > Begin FC step = 0 > Undisplaced coordinates > ============================== > > outcell: Unit cell vectors (Ang): > 15.846612 0.000000 0.000000 > 0.000000 15.842212 0.000000 > 0.000000 0.000000 5.669953 > > outcell: Cell vector modules (Ang) : 15.846612 15.842212 5.669953 > outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000 > outcell: Cell volume (Ang**3) : 1423.4155 > New_DM. Step: 1 > Initializing Density Matrix... > > InitMesh: MESH = 160 x 160 x 54 = 1382400 > InitMesh: Mesh cutoff (required, used) = 250.000 250.686 Ry > > * Maximum dynamic memory allocated = 166 MB > > stepf: Fermi-Dirac step function > > siesta: Program's energy decomposition (eV): > siesta: Ebs = -1549.643077 > siesta: Eions = 6359.269201 > siesta: Ena = 1347.446253 > siesta: Ekin = 2385.250061 > siesta: Enl = -47.350597 > siesta: DEna = -0.000004 > siesta: DUscf = 0.000000 > siesta: DUext = 0.000000 > siesta: Exc = -1199.686721 > siesta: eta*DQ = 0.000000 > siesta: Emadel = 0.000000 > siesta: Emeta = 0.000000 > siesta: Emolmec = 0.000000 > siesta: Ekinion = 0.000000 > siesta: Eharris = -3916.622480 > siesta: Etot = -3873.610208 > siesta: FreeEng = -3873.610208 > > siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) > siesta: 1 -3916.6225 -3873.6102 -3873.6102 1.9290 -5.3563 > timer: Routine,Calls,Time,% = IterSCF 1 13.645 94.28 > elaps: Routine,Calls,Wall,% = IterSCF 1 13.659 94.27 > siesta: 2 -3913.3349 -3907.1377 -3907.1377 0.1948 -2.3485 > siesta: 3 -3910.9739 -3908.2595 -3908.2595 0.1118 -2.5541 > siesta: 4 -3910.5063 -3908.8598 -3908.8598 0.0688 -2.9479 > siesta: 5 -3910.3910 -3909.2526 -3909.2526 0.0438 -3.1195 > siesta: 6 -3910.3585 -3909.5323 -3909.5323 0.0287 -3.2058 > siesta: 7 -3910.3480 -3909.7373 -3909.7373 0.0192 -3.2497 > siesta: 8 -3910.3442 -3909.8895 -3909.8895 0.0131 -3.2728 > siesta: 9 -3910.3427 -3910.0030 -3910.0030 0.0091 -3.2853 > siesta: 10 -3910.3422 -3910.0879 -3910.0879 0.0063 -3.2924 > siesta: 11 -3910.3419 -3910.1514 -3910.1514 0.0045 -3.2966 > siesta: 12 -3910.3418 -3910.1990 -3910.1990 0.0032 -3.2991 > siesta: 13 -3910.3418 -3910.2347 -3910.2347 0.0022 -3.3006 > siesta: 14 -3910.3417 -3910.2615 -3910.2615 0.0016 -3.3015 > siesta: 15 -3910.3417 -3910.2816 -3910.2816 0.0011 -3.3022 > siesta: 16 -3910.3417 -3910.2966 -3910.2966 0.0008 -3.3026 > siesta: 17 -3910.3417 -3910.3079 -3910.3079 0.0006 -3.3028 > siesta: 18 -3910.3417 -3910.3163 -3910.3163 0.0004 -3.3030 > siesta: 19 -3910.3417 -3910.3227 -3910.3227 0.0003 -3.3031 > siesta: 20 -3910.3417 -3910.3274 -3910.3274 0.0002 -3.3032 > siesta: 21 -3910.3417 -3910.3310 -3910.3310 0.0002 -3.3032 > siesta: 22 -3910.3417 -3910.3337 -3910.3337 0.0001 -3.3032 > siesta: 23 -3910.3417 -3910.3357 -3910.3357 0.0001 -3.3033 > grdsam: Reading %block GridCellSampling > grdsam: Grid-cell sampling, point 0 > grdsam: Generating displacements for grid-cell sampling > grdsam: Grid-cell sampling, point 1 > > siesta: E_KS(eV) = -3910.3370 > > siesta: E_KS - E_eggbox = -3910.3370 > > siesta: Atomic forces (eV/Ang): > ---------------------------------------- > Tot -0.000003 0.000036 -0.000000 > ---------------------------------------- > Max 1.290437 > Res 0.478146 sqrt( Sum f_i^2 / 3N ) > ---------------------------------------- > Max 1.290437 constrained > > Stress-tensor-Voigt (kbar): 14.20 14.38 -0.05 -0.00 > 0.00 -0.00 > (Free)E + p*V (eV/cell) -3918.7853 > Target enthalpy (eV/cell) -3910.3370 > > * Maximum dynamic memory allocated = 170 MB > > outcoor: Final (unrelaxed) atomic coordinates (Ang): > 1.25500000 3.55800000 0.00000000 1 1 C > 0.00000000 2.86400000 0.00000000 1 2 C > 0.00000000 1.43500000 0.00000000 1 3 C > 1.24300000 0.71800000 0.00000000 1 4 C > 2.48000000 1.43200000 0.00000000 1 5 C > 2.45400000 2.86600000 0.00000000 1 6 C > -1.24300000 0.71800000 0.00000000 1 7 C > 1.24300000 -0.71800000 0.00000000 1 8 C > 0.00000000 -1.43500000 0.00000000 1 9 C > -1.24300000 -0.71800000 0.00000000 1 10 C > 0.00000000 -2.86400000 0.00000000 1 11 C > 1.25500000 -3.55800000 0.00000000 1 12 C > 2.45400000 -2.86600000 0.00000000 1 13 C > 2.48000000 -1.43200000 0.00000000 1 14 C > 3.70900000 -0.69200000 0.00000000 1 15 C > 3.70900000 0.69200000 0.00000000 1 16 C > 4.64800000 1.24000000 0.00000000 2 17 H > 4.64800000 -1.24000000 0.00000000 2 18 H > 1.25000000 4.64600000 0.00000000 2 19 H > 3.39800000 3.40600000 0.00000000 2 20 H > 1.25000000 -4.64600000 0.00000000 2 21 H > 3.39800000 -3.40600000 0.00000000 2 22 H > -1.25500000 3.55800000 0.00000000 1 23 C > -2.45400000 2.86600000 0.00000000 1 24 C > -2.48000000 1.43200000 0.00000000 1 25 C > -1.25000000 4.64600000 0.00000000 2 26 H > -3.39800000 3.40600000 0.00000000 2 27 H > -3.70900000 0.69200000 0.00000000 1 28 C > -3.70900000 -0.69200000 0.00000000 1 29 C > -2.48000000 -1.43200000 0.00000000 1 30 C > -4.64800000 1.24000000 0.00000000 2 31 H > -4.64800000 -1.24000000 0.00000000 2 32 H > -1.25500000 -3.55800000 0.00000000 1 33 C > -1.25000000 -4.64600000 0.00000000 2 34 H > -2.45400000 -2.86600000 0.00000000 1 35 C > -3.39800000 -3.40600000 0.00000000 2 36 H > > coceri: Writing CERIUS coordinates into file coroneneFC.xtl > siesta: PDOS info: > siesta: e1, e2, sigma, nhist: -23.00 eV 50.00 eV 0.10 eV 1000 > > siesta: Program's energy decomposition (eV): > siesta: Ebs = -1308.502362 > siesta: Eions = 6359.269201 > siesta: Ena = 1347.446253 > siesta: Ekin = 2799.081707 > siesta: Enl = -390.559696 > siesta: DEna = -79.416911 > siesta: DUscf = 8.852200 > siesta: DUext = 0.000000 > siesta: Exc = -1236.471400 > siesta: eta*DQ = 0.000000 > siesta: Emadel = 0.000000 > siesta: Emeta = 0.000000 > siesta: Emolmec = 0.000000 > siesta: Ekinion = 0.000000 > siesta: Eharris = -3910.341718 > siesta: Etot = -3910.337047 > siesta: FreeEng = -3910.337047 > > siesta: Final energy (eV): > siesta: Band Struct. = -1308.502362 > siesta: Kinetic = 2799.081707 > siesta: Hartree = 11145.136325 > siesta: Ext. field = 0.000000 > siesta: Exch.-corr. = -1236.471400 > siesta: Ion-electron = -24781.493656 > siesta: Ion-ion = 8163.409977 > siesta: Ekinion = 0.000000 > siesta: Total = -3910.337047 > > siesta: Atomic forces (eV/Ang): > siesta: 1 -0.117292 -1.290433 0.000000 > siesta: 2 -0.000001 0.141799 0.000000 > siesta: 3 0.000000 -0.094679 0.000000 > siesta: 4 -0.110167 -0.093978 0.000000 > siesta: 5 0.153583 0.081283 -0.000000 > siesta: 6 -1.080285 -0.758036 -0.000000 > siesta: 7 0.110168 -0.093980 0.000000 > siesta: 8 -0.110163 0.093976 0.000000 > siesta: 9 -0.000001 0.094682 0.000000 > siesta: 10 0.110174 0.093981 0.000000 > siesta: 11 0.000001 -0.141793 -0.000000 > siesta: 12 -0.117292 1.290433 -0.000000 > siesta: 13 -1.080283 0.758035 -0.000000 > siesta: 14 0.153577 -0.081277 0.000000 > siesta: 15 -1.211917 0.544762 -0.000000 > siesta: 16 -1.211921 -0.544759 0.000000 > siesta: 17 0.485699 0.294311 0.000000 > siesta: 18 0.485699 -0.294311 -0.000000 > siesta: 19 -0.012723 0.538613 -0.000000 > siesta: 20 0.488439 0.263962 0.000000 > siesta: 21 -0.012723 -0.538614 0.000000 > siesta: 22 0.488440 -0.263962 -0.000000 > siesta: 23 0.117292 -1.290431 -0.000000 > siesta: 24 1.080282 -0.758034 -0.000000 > siesta: 25 -0.153577 0.081279 -0.000000 > siesta: 26 0.012723 0.538613 -0.000000 > siesta: 27 -0.488440 0.263963 0.000000 > siesta: 28 1.211919 -0.544756 -0.000000 > siesta: 29 1.211916 0.544762 -0.000000 > siesta: 30 -0.153584 -0.081272 -0.000000 > siesta: 31 -0.485700 0.294311 -0.000000 > siesta: 32 -0.485701 -0.294311 -0.000000 > siesta: 33 0.117289 1.290437 0.000000 > siesta: 34 0.012723 -0.538614 -0.000000 > siesta: 35 1.080282 0.758035 -0.000000 > siesta: 36 -0.488440 -0.263962 -0.000000 > siesta: ---------------------------------------- > siesta: Tot -0.000003 0.000036 -0.000000 > > siesta: Stress tensor (static) (eV/Ang**3): > siesta: 0.008863 -0.000000 -0.000000 > siesta: -0.000000 0.008976 0.000000 > siesta: -0.000000 0.000000 -0.000034 > > siesta: Cell volume = 1423.415527 Ang**3 > > siesta: Pressure (static): > siesta: Solid Molecule Units > siesta: -0.00006464 0.00000002 Ry/Bohr**3 > siesta: -0.00593522 0.00000201 eV/Ang**3 > siesta: -9.50938012 0.00322422 kBar > (Free)E+ p_basis*V_orbitals = -3900.512989 > (Free)Eharris+ p_basis*V_orbitals = -3900.519012 > > siesta: Electric dipole (a.u.) = 0.000000 0.000000 0.000000 > siesta: Electric dipole (Debye) = 0.000000 0.000001 0.000000 > > * Maximum dynamic memory allocated : Node 0 = 170 MB > > * Maximum memory occured during poison > > timer: CPU execution times: > timer: Routine Calls Time/call Tot.time % > timer: siesta 1 183.947 183.947 100.00 > timer: Setup 1 0.312 0.312 0.17 > timer: bands 1 0.000 0.000 0.00 > timer: writewave 1 0.000 0.000 0.00 > timer: KSV_init 1 0.000 0.000 0.00 > timer: IterMD 1 177.587 177.587 96.54 > timer: hsparse 1 0.100 0.100 0.05 > timer: overlap 1 0.412 0.412 0.22 > timer: IterSCF 23 6.351 146.069 79.41 > timer: kinefsm 2 0.246 0.492 0.27 > timer: nlefsm 2 1.000 2.000 1.09 > timer: DHSCF 25 6.721 168.023 91.34 > timer: DHSCF1 1 0.140 0.140 0.08 > timer: DHSCF2 2 5.568 11.137 6.05 > timer: REORD 204 0.004 0.860 0.47 > timer: POISON 27 0.303 8.185 4.45 > timer: DHSCF3 25 5.658 141.445 76.89 > timer: rhoofd 25 3.307 82.681 44.95 > timer: cellXC 25 0.297 7.420 4.03 > timer: vmat 24 1.704 40.903 22.24 > timer: MolMec 2 0.000 0.000 0.00 > timer: diagon 23 0.262 6.016 3.27 > timer: r-eigvec 23 0.246 5.668 3.08 > timer: r-buildHS 23 0.002 0.044 0.02 > timer: rdiag 24 0.245 5.868 3.19 > timer: rdiag1 24 0.012 0.292 0.16 > timer: rdiag2 24 0.035 0.832 0.45 > timer: rdiag3 24 0.158 3.784 2.06 > timer: rdiag4 24 0.040 0.948 0.52 > timer: r-buildD 23 0.014 0.332 0.18 > timer: DHSCF4 2 7.482 14.965 8.14 > timer: dfscf 2 6.744 13.489 7.33 > timer: overfsm 1 0.088 0.088 0.05 > timer: pdos 1 6.036 6.036 3.28 > timer: optical 1 0.000 0.000 0.00 > > > elaps: ELAPSED times: > elaps: Routine Calls Time/call Tot.time % > elaps: siesta 1 184.082 184.082 100.00 > elaps: Setup 1 0.311 0.311 0.17 > elaps: bands 1 0.000 0.000 0.00 > elaps: writewave 1 0.002 0.002 0.00 > elaps: KSV_init 1 0.000 0.000 0.00 > elaps: IterMD 1 177.718 177.718 96.54 > elaps: hsparse 1 0.097 0.097 0.05 > elaps: overlap 1 0.412 0.412 0.22 > elaps: IterSCF 23 6.356 146.177 79.41 > elaps: kinefsm 2 0.244 0.489 0.27 > elaps: nlefsm 2 1.002 2.003 1.09 > elaps: DHSCF 25 6.725 168.137 91.34 > elaps: DHSCF1 1 0.140 0.140 0.08 > elaps: DHSCF2 2 5.576 11.153 6.06 > elaps: REORD 204 0.004 0.879 0.48 > elaps: POISON 27 0.303 8.194 4.45 > elaps: DHSCF3 25 5.661 141.527 76.88 > elaps: rhoofd 25 3.309 82.720 44.94 > elaps: cellXC 25 0.297 7.436 4.04 > elaps: vmat 24 1.705 40.919 22.23 > elaps: MolMec 2 0.000 0.000 0.00 > elaps: diagon 23 0.262 6.020 3.27 > elaps: r-eigvec 23 0.247 5.673 3.08 > elaps: r-buildHS 23 0.002 0.048 0.03 > elaps: rdiag 24 0.245 5.870 3.19 > elaps: rdiag1 24 0.012 0.296 0.16 > elaps: rdiag2 24 0.035 0.830 0.45 > elaps: rdiag3 24 0.158 3.788 2.06 > elaps: rdiag4 24 0.039 0.943 0.51 > elaps: r-buildD 23 0.014 0.333 0.18 > elaps: DHSCF4 2 7.487 14.974 8.13 > elaps: dfscf 2 6.747 13.494 7.33 > elaps: overfsm 1 0.087 0.087 0.05 > elaps: pdos 1 6.040 6.040 3.28 > elaps: optical 1 0.000 0.000 0.00 > > >> End of run: 24-AUG-2015 8:40:01 > > ====================== FC =============================== > > Force constants matrix > > >
