You should define MD.FCfirst & MD.FClast for the first atom and the last one you want to displace. In your input file, you do not define the last atom "MD.FClast 0"
On Mon, Aug 24, 2015 at 9:35 AM, Nick Papior <[email protected]> wrote: > 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 >> >> >>
