--- Code logo: "__________________________________ A fast and precise DFT wavelet code | | | | | | | | | | | | BBBB i gggggg |_____|_____|_____|_____|_____| B B g | | : | : | | | B B i g | |-0+--|-0+--| | | B B i g g |_____|__:__|__:__|_____|_____|___ BBBBB i g g | : | | | : | | B B i g g |--+0-| | |-0+--| | B B iiii g g |__:__|_____|_____|__:__|_____| B B i g g | | : | : | | | B BBBB i g g | |-0+--|-0+--| | | B iiiii gggggg |_____|__:__|__:__|_____|_____|__BBBBB | | | | : | | TTTTTTTTT | | | |--+0-| | DDDDDD FFFFF T |_____|_____|_____|__:__|_____| D D F TTTT T | | | | : | |D D F T T | | | |--+0-| |D D FFFF T T |_____|_____|_____|__:__|_____|D___ D F T T | | | : | | |D D F TTTTT | | |--+0-| | | D D F T T |_____|_____|__:__|_____|_____| D F T T | | | | | | D T T | | | | | | DDDDDD F TTTT |_____|_____|_____|_____|_____|______ www.bigdft.org " Reference Paper : The Journal of Chemical Physics 129, 014109 (2008) Version Number : 1.8.2 Timestamp of this run : 2018-12-06 11:37:00.000 Root process Hostname : localhost Number of MPI tasks : 1 OpenMP parallelization : No #------------------------------------------------------------------ Code compiling options Compilation options: Configure arguments: " '--prefix' '/home/tohoyn/src/bigdft/build/install' 'FC=gfortran' 'CC=gcc' 'FCFLAGS=-O2 -Wno-error -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow -g -Wl,--no-as-needed -ldl' '--enable-devel-doc' 'LDFLAGS=-L/home/tohoyn/src/bigdft/build/install/lib ' 'C_INCLUDE_PATH=/home/tohoyn/src/bigdft/build/install/include' 'PKG_CONFIG_PATH=/home/tohoyn/src/bigdft/build/install/lib/pkgconfig:/home/tohoyn/src/bi gdft/build/install/share/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgconfi g:/usr/share/pkgconfig'" Compilers (CC, FC, CXX) : [ gcc, gfortran, g++ ] Compiler flags: CFLAGS : -g -O2 FCFLAGS: -O2 -Wno-error -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow -g -Wl,--no-as-needed -ldl CXXFLAGS : -g -O2 #------------------------------------------------------------------------ Input parameters radical : null outdir : ./ logfile : Yes run_from_files : Yes skip : No dft: hgrids : 0.45 # Grid spacing in the three directions (bohr) gnrm_cv : 1.e-7 # Convergence criterion gradient rmult: [3.000000000000, 7.0] # c(f)rmult*radii_cf(:,1(2))=coarse(fine) atom-based radius qcharge : 1 # Charge of the system. Can be integer or real. nspin : 2 # Spin polarization treatment mpol : 1 # Total magnetic moment ixc : 1000 # Exchange-correlation parameter (LDA=1,PBE=11) itermax : 100 # Max. iterations of wfn. opt. steps disablesym : Yes # Disable the symmetry detection ngrids: [0, 0, 0] # Number of grid spacing division in each direction elecfield: [0., 0., 0.] # Electric field (Ex,Ey,Ez) itermin : 0 # Minimal iterations of wfn. optimized steps nrepmax : 1 # Max. number of re-diag. runs ncong : 6 # No. of CG it. for preconditioning eq. idsx : 6 # Wfn. diis history dispersion : 0 # Dispersion correction potential (values 1,2,3,4,5), 0=none inputpsiid : 0 # Input guess wavefunctions output_denspot : 0 # Output of the density or the potential rbuf : 0. # Length of the tail (AU) ncongt : 30 # No. of tail CG iterations norbv : 0 # Davidson subspace dimension (No. virtual orbitals) nvirt : 0 # No. of converged virtual orbs (< norbv) nplot : 0 # No. of plotted orbs gnrm_cv_virt : 1.e-4 # Convergence criterion gradient for virtual orbitals itermax_virt : 50 # Max. iterations of wfn. opt. steps for virtual orbitals external_potential : 0.0 # Multipole moments of an external potential calculate_strten : Yes # Boolean to activate the calculation of the stress tensor. Might be set to No for # performance reasons plot_mppot_axes: [-1, -1, -1] # Plot the potential generated by the multipoles along axes through this # point. Negative values mean no plot. plot_pot_axes: [-1, -1, -1] # Plot the potential along axes through this point. Negative values mean # no plot. occupancy_control : None # Dictionary of the atomic matrices to be applied for a given iteration number itermax_occ_ctrl : 0 # Number of iterations of occupancy control scheme. Should be between itermin and # itermax nrepmax_occ_ctrl : 1 # Number of re-diagonalizations of occupancy control scheme. alpha_hf : -1.0 # Part of the exact exchange contribution for hybrid functionals perf: exctxpar : BC # Exact exchange parallelisation scheme debug : No # Debug option fftcache : 8192 # Cache size for the FFT accel : NO # Acceleration (hardware) ocl_platform : ~ # Chosen OCL platform ocl_devices : ~ # Chosen OCL devices blas : No # CUBLAS acceleration projrad : 15. # Radius of the projector as a function of the maxrad ig_diag : Yes # Input guess (T=Direct, F=Iterative) diag. of Ham. ig_norbp : 5 # Input guess Orbitals per process for iterative diag. ig_blocks: [300, 800] # Input guess Block sizes for orthonormalisation ig_tol : 1.0e-4 # Input guess Tolerance criterion methortho : 0 # Orthogonalisation rho_commun : DEF # Density communication scheme (DBL, RSC, MIX) unblock_comms : OFF # Overlap Communications of fields (OFF,DEN,POT) linear : OFF # Linear Input Guess approach tolsym : 1.0e-8 # Tolerance for symmetry detection signaling : No # Expose calculation results on Network signaltimeout : 0 # Time out on startup for signal connection (in seconds) domain : ~ # Domain to add to the hostname to find the IP inguess_geopt : 0 # Input guess to be used during the optimization store_index : Yes # Store indices or recalculate them for linear scaling psp_onfly : Yes # Calculate pseudopotential projectors on the fly multipole_preserving : No # (EXPERIMENTAL) Preserve the multipole moment of the ionic density mp_isf : 16 # (EXPERIMENTAL) Interpolating scaling function or lifted dual order for the multipole # preserving mixing_after_inputguess : 1 # Mixing step after linear input guess iterative_orthogonalization : No # Iterative_orthogonalization for input guess orbitals check_sumrho : 1 # Enables linear sumrho check check_overlap : 1 # Enables linear overlap check experimental_mode : No # Activate the experimental mode in linear scaling explicit_locregcenters : No # Linear scaling explicitly specify localization centers calculate_KS_residue : Yes # Linear scaling calculate Kohn-Sham residue intermediate_forces : No # Linear scaling calculate intermediate forces kappa_conv : 0.1 # Exit kappa for extended input guess (experimental mode) calculate_gap : No # Linear scaling calculate the HOMO LUMO gap loewdin_charge_analysis : No # Linear scaling perform a Loewdin charge analysis at the end of the calculation coeff_weight_analysis : No # Linear scaling perform a Loewdin charge analysis of the coefficients for fragment # calculations check_matrix_compression : Yes # Linear scaling perform a check of the matrix compression routines correction_co_contra : Yes # Linear scaling correction covariant / contravariant gradient FOE_restart : 0 # Restart method to be used for the FOE method imethod_overlap : 1 # Method to calculate the overlap matrices (1=old, 2=new) enable_matrix_taskgroups : True # Enable the matrix taskgroups hamapp_radius_incr : 8 # Radius enlargement for the Hamiltonian application (in grid points) adjust_kernel_iterations : True # Enable the adaptive ajustment of the number of kernel iterations adjust_kernel_threshold : True # Enable the adaptive ajustment of the kernel convergence threshold according to the # support function convergence wf_extent_analysis : False # Perform an analysis of the extent of the support functions (and possibly KS orbitals) foe_gap : False # Use the FOE method to calculate the HOMO-LUMO gap at the end of a calculation geopt: method : BFGS # Geometry optimisation method ncount_cluster_x : 20 # Maximum number of force evaluations frac_fluct : 5.0 # Fraction of force fluctuations. Stop if fmax < forces_fluct*frac_fluct randdis : 0.0 # Random displacement amplitude betax : 4.0 # Stepsize for the geometry optimization forcemax : 0. # Max forces criterion when stop beta_stretchx : 5e-1 # Stepsize for steepest descent in stretching mode direction (only if in biomode) psppar.H: Pseudopotential type : HGH Atomic number : 1 No. of Electrons : 1 Pseudopotential XC : 1000 Local Pseudo Potential (HGH convention): Rloc : 0.2 Coefficients (c1 .. c4): [-4.180237, 0.725075, 0.0, 0.0] Radii of active regions (AU): Coarse : 1.463418464633951 Fine : 0.2 Coarse PSP : 0.0 Source : PSP File psolver: kernel: screening : 0 # Mu screening parameter isf_order : 16 # Order of the Interpolating Scaling Function family stress_tensor : Yes # Triggers the calculation of the stress tensor environment: cavity : none # Type of the cavity fd_order : 16 # Order of the Finite-difference derivatives for the GPS solver itermax : 200 # Maximum number of iterations of the GPS outer loop minres : 1.e-8 # Convergence threshold of the loop pb_method : none # Defines the method for the Poisson Boltzmann Equation setup: accel : none # Material Acceleration taskgroup_size : 0 # Size of the taskgroups of the Poisson Solver global_data : No # Charge density and Electrostatic potential are given by global arrays verbose : Yes # Verbosity switch output : none # Quantities to be plotted after the main solver routine chess: foe: ef_interpol_det : 1.e-12 # FOE max determinant of cubic interpolation matrix ef_interpol_chargediff : 1.0 # FOE max charge difference for interpolation evbounds_nsatur : 3 # Number of FOE cycles before the eigenvalue bounds are shrinked (linear) evboundsshrink_nsatur : 4 # Maximal number of unsuccessful eigenvalue bounds shrinkings fscale : 5.e-2 # Initial guess for the error function decay length fscale_lowerbound : 5.e-3 # Lower bound for the error function decay length fscale_upperbound : 5.e-2 # Upper bound for the error function decay length eval_range_foe: [-0.5, 0.5] # Lower and upper bound of the eigenvalue spectrum, will be adjusted # automatically if chosen unproperly accuracy_foe : 1.e-5 # Required accuracy for the Chebyshev fit for FOE accuracy_ice : 1.e-8 # Required accuracy for the Chebyshev fit for ICE (calculation of matrix powers) accuracy_penalty : 1.e-5 # Required accuracy for the Chebyshev fit for the penalty function accuracy_entropy : 1.e-4 # Required accuracy for the Chebyshev fit for the function to calculate the entropy term betax_foe : -1000.0 # the exponent in the exponential penalty function which is used to determine the # eigenvalue bounds for FOE betax_ice : -1000.0 # the exponent in the exponential penalty function which is used to determine the # eigenvalue bounds for ICE occupation_function : 102 # the function to assign the occupation numbers adjust_fscale : yes # dynamically adjust the value of fscale or not matmul_optimize_load_balancing : no # optimize the load balancing of the sparse matrix matrix multiplications (at the cost # of memory unbalancing) fscale_ediff_low : 5.e-5 # lower bound for the optimal relative energy difference between the kernel and the # control kernel fscale_ediff_up : 1.e-4 # upper bound for the optimal relative energy difference between the kernel and the # control kernel lapack: blocksize_pdsyev : -8 # SCALAPACK linear scaling blocksize for diagonalization blocksize_pdgemm : -8 # SCALAPACK linear scaling blocksize for matrix matrix multiplication maxproc_pdsyev : 4 # SCALAPACK linear scaling max num procs maxproc_pdgemm : 4 # SCALAPACK linear scaling max num procs pexsi: pexsi_npoles : 40 # Number of poles used by PEXSI pexsi_nproc_per_pole : 1 # Number of processes used per pole by PEXSI pexsi_mumin : -1.0 # Initial guess for the lower bound of the chemical potential used by PEXSI pexsi_mumax : 1.0 # Initial guess for the upper bound of the chemical potential used by PEXSI pexsi_mu : 0.5 # Initial guess for the chemical potential used by PEXSI pexsi_temperature : 1.e-3 # Temperature used by PEXSI pexsi_tol_charge : 1.e-3 # Charge tolerance used PEXSI pexsi_np_sym_fact : 16 # Number of tasks for the symbolic factorization used by PEXSI pexsi_DeltaE : 10.0 # Upper bound for the spectral radius of S^-1H (in hartree?) used by PEXSI pexsi_do_inertia_count : yes # Decides whether PEXSI should use the inertia count at each iteration pexsi_max_iter : 10 # Maximal number of PEXSI iterations pexsi_verbosity : 0 # Verbosity level of the PEXSI solver output: verbosity : 2 # Verbosity of the output atomic_density_matrix : None # Dictionary of the atoms for which the atomic density matrix has to be plotted sdos : No # Spatially-resolved density of states orbitals : No # Write KS orbitals in the full simulation domain (might take lot of disk space!) outputpsiid : wavefunction # basename of the output wavefunctions files written in the data directory kpt: method : manual # K-point sampling method kpt: # Kpt coordinates - [0., 0., 0.] wkpt: [1.] # Kpt weights bands : No # For doing band structure calculation md: mdsteps : 0 # Number of MD steps print_frequency : 1 # Printing frequency for energy.dat and Trajectory.xyz files temperature : 300.d0 # Initial temperature in Kelvin timestep : 20.d0 # Time step for integration (in a.u.) no_translation : No # Logical input to set translational correction thermostat : none # Activates a thermostat for MD wavefunction_extrapolation : 0 # Activates the wavefunction extrapolation for MD always_from_scratch : No # When true, always restart wavefunctions from scratch to eliminate dissipation effects restart_nose : No # Restart Nose Hoover Chain information from md.restart restart_pos : No # Restart nuclear position information from md.restart restart_vel : No # Restart nuclear velocities information from md.restart mix: iscf : 0 # Mixing scheme (default=0 i.e. direct minimization) itrpmax : 1 # Maximum number of diagonalisation iterations rpnrm_cv : 1.e-4 # Stop criterion on the residue of potential or density norbsempty : 0 # No. of additional bands tel : 0. # Electronic temperature occopt : 1 # Smearing method alphamix : 0. # Multiplying factors for the mixing alphadiis : 2. # Multiplying factors for the electronic DIIS sic: sic_approach : none # SIC (self-interaction correction) method sic_alpha : 0. # SIC downscaling parameter tddft: tddft_approach : none # Time-Dependent DFT method decompose_perturbation : none # Indicate the directory of the perturbation to be decomposed in the basis of empty # states mode: method : dft # Run method of BigDFT call add_coulomb_force : No # Boolean to add coulomb force on top of any of above selected force lin_general: hybrid : No # Activate the hybrid mode; if activated, only the low accuracy values will be relevant nit: [100, 100] # Number of iteration with low/high accuracy rpnrm_cv: [1.e-12, 1.e-12] # Convergence criterion for low/high accuracy conf_damping : -0.5 # How the confinement should be decreased, only relevant for hybrid mode; negative -> # automatic taylor_order : 0 # Order of the Taylor approximation; 0 -> exact max_inversion_error : 1.d0 # Linear scaling maximal error of the Taylor approximations to calculate the inverse of # the overlap matrix output_wf : 0 # Output basis functions; 0 no output, 1 formatted output, 2 Fortran bin, 3 ETSF output_mat : 0 # Output sparse matrices; 0 no output, 1 formatted sparse, 11 formatted dense, 21 # formatted both output_coeff : 0 # Output KS coefficients; 0 no output, 1 formatted output output_fragments : 0 # Output support functions, kernel and coeffs; 0 fragments and full system, 1 # fragments only, 2 full system only kernel_restart_mode : 0 # Method for restarting kernel; 0 kernel, 1 coefficients, 2 random, 3 diagonal, 4 # support function weights kernel_restart_noise : 0.0d0 # Add random noise to kernel or coefficients when restarting frag_num_neighbours : 0 # Number of neighbours to output for each fragment frag_neighbour_cutoff : 12.0d0 # Number of neighbours to output for each fragment cdft_lag_mult_init : 0.05d0 # CDFT initial value for Lagrange multiplier cdft_conv_crit : 1.e-2 # CDFT convergence threshold for the constrained charge calc_dipole : No # Calculate dipole calc_quadrupole : No # Calculate quadrupole subspace_diag : No # Diagonalization at the end extra_states : 0 # Number of extra states to include in support function and kernel optimization (dmin # only), must be equal to norbsempty calculate_onsite_overlap : No # Calculate the onsite overlap matrix (has only an effect if the matrices are all # written to disk) charge_multipoles : 0 # Calculate the atom-centered multipole coefficients; 0 no, 1 old approach Loewdin, 2 # new approach Projector support_function_multipoles : False # Calculate the multipole moments of the support functions plot_locreg_grids : False # Plot the scaling function and wavelets grid of each localization region calculate_FOE_eigenvalues: [0, -1] # First and last eigenvalue to be calculated using the FOE procedure precision_FOE_eigenvalues : 5.e-3 # Decay length of the error function used to extract the eigenvalues (i.e. something like # the resolution) multipole_centers : 0.0 # Determines whether the multipole centers shall be determined automatically (i.e. # taking the atoms) or whether they are # provided manually consider_entropy : False # Indicate whether the entropy contribution to the total energy shall be considered lin_basis: nit: [4, 5] # Maximal number of iterations in the optimization of the # support functions nit_ig : 50 # maximal number of iterations to optimize the support functions in the extended input # guess (experimental mode only) idsx: [6, 6] # DIIS history for optimization of the support functions # (low/high accuracy); 0 -> SD gnrm_cv: [1.e-2, 1.e-4] # Convergence criterion for the optimization of the support functions # (low/high accuracy) gnrm_ig : 1.e-3 # Convergence criterion for the optimization of the support functions in the extended # input guess (experimental mode only) deltae_cv : 1.e-4 # Total relative energy difference to stop the optimization ('experimental_mode' only) gnrm_dyn : 1.e-4 # Dynamic convergence criterion ('experimental_mode' only) min_gnrm_for_dynamic : 1.e-3 # Minimal gnrm to active the dynamic gnrm criterion alpha_diis : 1.0 # Multiplicator for DIIS alpha_sd : 1.0 # Initial step size for SD nstep_prec : 5 # Number of iterations in the preconditioner fix_basis : 1.e-10 # Fix the support functions if the density change is below this threshold correction_orthoconstraint : 1 # Correction for the slight non-orthonormality in the orthoconstraint orthogonalize_ao : Yes # Orthogonalize the atomic orbitals used as input guess reset_DIIS_history : No # Reset the DIIS history when starting the loop which optimizes the support functions lin_kernel: nstep: [1, 1] # Number of steps taken when updating the coefficients via # direct minimization for each iteration of # the density kernel loop nit: [5, 5] # Number of iterations in the (self-consistent) # optimization of the density kernel idsx_coeff: [0, 0] # DIIS history for direct mininimization idsx: [0, 0] # Mixing method; 0 -> linear mixing, >=1 -> Pulay mixing alphamix: [0.5, 0.5] # Mixing parameter (low/high accuracy) gnrm_cv_coeff: [1.e-5, 1.e-5] # Convergence criterion on the gradient for direct minimization rpnrm_cv: [1.e-10, 1.e-10] # Convergence criterion (change in density/potential) for the kernel # optimization linear_method : DIAG # Method to optimize the density kernel mixing_method : DEN # Quantity to be mixed alpha_sd_coeff : 0.2 # Initial step size for SD for direct minimization alpha_fit_coeff : No # Update the SD step size by fitting a quadratic polynomial coeff_scaling_factor : 1.0 # Factor to scale the gradient in direct minimization delta_pnrm : -1.0 # Stop the kernel optimization if the density/potential difference has decreased by this # factor (deactivated if -1.0) lin_basis_params: nbasis : 4 # Number of support functions per atom ao_confinement : 8.3e-3 # Prefactor for the input guess confining potential confinement: [8.3e-3, 0.0] # Prefactor for the confining potential (low/high accuracy) rloc: [7.0, 7.0] # Localization radius for the support functions rloc_kernel : 9.0 # Localization radius for the density kernel rloc_kernel_foe : 14.0 # Cutoff radius for the FOE matrix vector multiplications posinp: #---------------------------------------------- Atomic positions (by default bohr units) positions: - H: [0.0, 0.0, 1.0] IGSpin : 1 - H: [0.0, 0.0, -1.0] IGSpin : 0 properties: format : yaml source : input.yaml #--------------------------------------------------------------------------------------- | Data Writing directory : ./data/ #-------------------------------------------------- Input Atomic System (file: input.yaml) Atomic System Properties: Number of atomic types : 1 Number of atoms : 2 Types of atoms : [ H ] Boundary Conditions : Free #Code: F Number of Symmetries : 0 Space group : disabled #-------------------------------------------------- Geometry optimization Input Parameters Geometry Optimization Parameters: Maximum steps : 20 Algorithm : BFGS Random atomic displacement : 0.0E+00 Fluctuation in forces : 5.0E+00 Maximum in forces : 0.0E+00 Steepest descent step : 4.0E+00 Material acceleration : No #iproc=0 #------------------------------------------------------------------------ Input parameters DFT parameters: eXchange Correlation: XC ID : &ixc 1000 Exchange-Correlation reference : "No Hartree and XC terms" XC functional implementation : ABINIT Polarisation : 1 Spin polarization : collinear Net Charge (Ions-Electrons) : 1.00000 Basis set definition: Suggested Grid Spacings (a0) : [ 0.45, 0.45, 0.45 ] Coarse and Fine Radii Multipliers : [ 3.0, 7.0 ] Self-Consistent Cycle Parameters: Wavefunction: Gradient Norm Threshold : &gnrm_cv 1.0E-07 CG Steps for Preconditioner : 6 DIIS History length : 6 Max. Wfn Iterations : &itermax 100 Max. Subspace Diagonalizations : 1 Input wavefunction policy : INPUT_PSI_LCAO # 0 Output wavefunction policy : NONE # 0 Output grid policy : NONE # 0 Virtual orbitals : 0 Number of plotted density orbitals: 0 Density/Potential: Max. Iterations : 1 Post Optimization Parameters: Finite-Size Effect estimation: Scheduled : No #----------------------------------------------------------------------- System Properties Properties of atoms in the system: - Symbol : H #Type No. 01 No. of Electrons : 1 No. of Atoms : 2 Radii of active regions (AU): Coarse : 1.46342 Fine : 0.20000 Coarse PSP : 0.00000 Source : PSP File Grid Spacing threshold (AU) : 0.50 Pseudopotential type : HGH Local Pseudo Potential (HGH convention): Rloc : 0.20000 Coefficients (c1 .. c4) : [ -4.18024, 0.72508, 0.00000, 0.00000 ] No. of projectors : 0 PSP XC : "No Hartree and XC terms" #----------------------------------------------- Atom Positions (specified and grid units) Atomic structure: Units : bohr Positions: - {H: [ 4.275000000, 4.275000000, 6.175000000], # [ 9.50, 9.50, 13.72 ] 0001 IGSpin: 1} - H: [ 4.275000000, 4.275000000, 4.175000000] # [ 9.50, 9.50, 9.28 ] 0002 Rigid Shift Applied (AU) : [ 4.2750, 4.2750, 5.1750 ] #------------------------------------------------------------------------- Grid properties Box Grid spacings : [ 0.4500, 0.4500, 0.4500 ] Sizes of the simulation domain: AU : [ 8.5500, 8.5500, 10.350 ] Angstroem : [ 4.5245, 4.5245, 5.4770 ] Grid Spacing Units : [ 19, 19, 23 ] High resolution region boundaries (GU): From : [ 7, 7, 7 ] To : [ 12, 12, 16 ] High Res. box is treated separately : Yes Wavefunctions Descriptors, full simulation domain: Coarse resolution grid: No. of segments : 384 No. of points : 5176 Fine resolution grid: No. of segments : 56 No. of points : 248 #------------------------------------------------------------------- Kernel Initialization Poisson Kernel Initialization: #---------------------------------------------------------------------- Input parameters kernel: screening : 0 # Mu screening parameter isf_order : 16 # Order of the Interpolating Scaling Function family stress_tensor : Yes # Triggers the calculation of the stress tensor environment: cavity : none # Type of the cavity fd_order : 16 # Order of the Finite-difference derivatives for the GPS solver itermax : 200 # Maximum number of iterations of the GPS outer loop minres : 1.e-8 # Convergence threshold of the loop pb_method : none # Defines the method for the Poisson Boltzmann Equation setup: accel : none # Material Acceleration taskgroup_size : 0 # Size of the taskgroups of the Poisson Solver global_data : No # Charge density and Electrostatic potential are given by global arrays verbose : Yes # Verbosity switch output : none # Quantities to be plotted after the main solver routine MPI tasks : 1 Poisson Kernel Creation: Boundary Conditions : Free Memory Requirements per MPI task: Density (MB) : 2.99 Kernel (MB) : 3.12 Full Grid Arrays (MB) : 2.80 #------------------------------------------------------- Electronic Orbital Initialization Total Number of Electrons : 1 Spin treatment : Collinear Orbitals Repartition: MPI tasks 0- 0 : 1 Total Number of Orbitals : 1 Input Occupation Numbers: - Occupation Numbers: {Orbital No. 1: 1.0000} Wavefunctions memory occupation for root MPI process: 0 MB 54 KB 0 B NonLocal PSP Projectors Descriptors: Creation strategy : On-the-fly Total number of projectors : 0 Total number of components : 0 Percent of zero components : 0 Communication checks: Transpositions : Yes Reverse transpositions : Yes #-------------------------------------------------------- Estimation of Memory Consumption Memory requirements for principal quantities (MiB.KiB): Subspace Matrix : 0.1 # (Number of Orbitals: 1) Single orbital : 0.54 # (Number of Components: 6912) All (distributed) orbitals : 0.108 # (Number of Orbitals per MPI task: 1) Wavefunction storage size : 0.756 # (DIIS/SD workspaces included) Nonlocal Pseudopotential Arrays : 0.0 Full Uncompressed (ISF) grid : 5.609 Workspaces storage size : 0.169 Accumulated memory requirements during principal run stages (MiB.KiB): Kernel calculation : 34.275 Density Construction : 28.624 Poisson Solver : 51.723 Hamiltonian application : 28.727 Orbitals Orthonormalization : 28.727 Estimated Memory Peak (MB) : 51 Ion-Ion interaction energy : 5.00000000000000E-01 #---------------------------------------------------------------- Ionic Potential Creation Total ionic charge : -2.000000714589 Poisson Solver: BC : Free Box : [ 69, 69, 77 ] MPI tasks : 1 Interaction energy ions multipoles : 0.0 Interaction energy multipoles multipoles: 0.0 #----------------------------------- Wavefunctions from PSP Atomic Orbitals Initialization Input Hamiltonian: Total No. of Atomic Input Orbitals : 4 Atomic Input Orbital Generation: - {Atom Type: H, Electronic configuration: { s: [ 1.00, 0.00]}} - {Atom Type: H, Electronic configuration: { s: [ 0.50, 0.50]}} Wavelet conversion succeeded : Yes Deviation from normalization : 1.38E-06 Expected kinetic energy : 1.8316155336 Energies: {Ekin: 1.83170132597E+00, Epot: -3.66164490239E+00} EKS : -1.32994357641989369E+00 Input Guess Overlap Matrices: {Calculated: Yes, Diagonalized: Yes} Total magnetization : 1.000000 #Eigenvalues and New Occupation Numbers Orbitals: [ {e: -1.072333558819E+00, f: 1.0000, s: 1}, {e: -1.072333558819E+00, f: 0.0000, s: -1}, # 00001 {e: -5.924743528669E-01, f: 0.0000, s: 1}, {e: -5.924743528669E-01, f: 0.0000, s: -1}] # 00002 IG wavefunctions defined : Yes Accuracy estimation for this run: Energy : 8.58E-05 Convergence Criterion : 8.58E-05 #------------------------------------------------------------------- Self-Consistent Cycle Ground State Optimization: - Hamiltonian Optimization: &itrp001 - Subspace Optimization: &itrep001-01 Wavefunctions Iterations: - { #---------------------------------------------------------------------- iter: 1 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 7.33789039495E-01, Epot: -1.80612259831E+00}, iter: 1, EKS: -5.72333558818650889E-01, gnrm: 2.10E-01, DIIS weights: [ 1.00E+00, 1.00E+00], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 2 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.64153722524E-01, Epot: -1.75986207137E+00}, iter: 2, EKS: -5.95708348846682334E-01, gnrm: 9.21E-02, DIIS weights: [-7.02E-01, 1.70E+00, -1.29E-04], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 3 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.14131599563E-01, Epot: -1.71560820930E+00}, iter: 3, EKS: -6.01476609736697032E-01, gnrm: 2.22E-02, DIIS weights: [ 1.47E-01, -4.28E-01, 1.28E+00, -1.07E-05], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 4 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.07322935420E-01, Epot: -1.70891248600E+00}, iter: 4, EKS: -6.01589550584521238E-01, gnrm: 5.29E-03, DIIS weights: [-1.11E-02, 4.32E-02, -3.93E-01, 1.36E+00, -1.51E-07], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 5 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05794325910E-01, Epot: -1.70738984906E+00}, iter: 5, EKS: -6.01595523154043299E-01, gnrm: 6.72E-04, DIIS weights: [ 1.38E-03, -5.73E-03, 6.22E-02, -2.62E-01, 1.20E+00, -2.74E-09], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 6 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05783537921E-01, Epot: -1.70737909931E+00}, iter: 6, EKS: -6.01595561390602107E-01, gnrm: 1.26E-04, DIIS weights: [ 6.24E-04, -1.47E-03, -2.12E-03, 2.30E-02, -2.41E-01, 1.22E+00, -2.78E-10], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 7 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05798132643E-01, Epot: -1.70739369626E+00}, iter: 7, EKS: -6.01595563617538520E-01, gnrm: 3.27E-05, DIIS weights: [ 1.54E-04, -1.51E-03, 4.84E-03, 3.97E-02, -8.17E-01, 1.77E+00, -6.04E-11], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 8 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05812088000E-01, Epot: -1.70740765240E+00}, iter: 8, EKS: -6.01595564399278970E-01, gnrm: 1.75E-05, DIIS weights: [-7.87E-04, 3.43E-03, -2.81E-02, 3.41E-01, -1.05E+00, 1.73E+00, -1.87E-11], Orthogonalization Method: 0} - { #---------------------------------------------------------------------- iter: 9 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05813810357E-01, Epot: -1.70740937499E+00}, iter: 9, EKS: -6.01595564628184754E-01, gnrm: 9.25E-06, DIIS weights: [ 5.50E-04, -7.70E-04, -1.33E-01, 6.91E-01, -2.17E+00, 2.61E+00, -1.76E-12], Orthogonalization Method: 0} - { #--------------------------------------------------------------------- iter: 10 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05811511435E-01, Epot: -1.70740707616E+00}, iter: 10, EKS: -6.01595564722530174E-01, gnrm: 2.80E-06, DIIS weights: [-3.54E-04, 2.59E-02, -1.44E-01, 5.20E-01, -7.84E-01, 1.38E+00, -1.44E-13], Orthogonalization Method: 0} - { #--------------------------------------------------------------------- iter: 11 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05811311260E-01, Epot: -1.70740687598E+00}, iter: 11, EKS: -6.01595564724896725E-01, gnrm: 6.40E-07, DIIS weights: [-2.90E-04, 1.10E-02, -7.17E-02, 1.47E-01, -5.48E-01, 1.46E+00, -1.22E-14], Orthogonalization Method: 0} - { #--------------------------------------------------------------------- iter: 12 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05811386122E-01, Epot: -1.70740695085E+00}, iter: 12, EKS: -6.01595564725028620E-01, gnrm: 1.40E-07, DIIS weights: [-1.08E-03, 1.01E-02, -2.34E-02, 1.31E-01, -5.62E-01, 1.45E+00, -1.02E-15], Orthogonalization Method: 0} - { #--------------------------------------------------------------------- iter: 13 Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes, Energies: {Ekin: 6.05811404761E-01, Epot: -1.70740696949E+00}, iter: 13, EKS: -6.01595564725063481E-01, gnrm: 4.73E-08, DIIS weights: [-2.08E-04, 8.61E-04, -2.32E-02, 1.50E-01, -6.67E-01, 1.54E+00, -5.59E-17], Orthogonalization Method: 0} - &FINAL001 { #---------------------------------------------------------- iter: 14 Hamiltonian Applied: Yes, iter: 14, EKS: -6.01595564725052157E-01, gnrm: 4.73E-08, #FINAL Energies: {Ekin: 6.05811402316E-01, Epot: -1.70740696704E+00, Eion: 5.00000000000E-01}, } Non-Hermiticity of Hamiltonian in the Subspace: 0.00E+00 Total magnetization : 1.000000 #Eigenvalues and New Occupation Numbers Orbitals: [ {e: -1.101595564725E+00, f: 1.0000, s: 1}] # 00001 Last Iteration : *FINAL001 #---------------------------------------------------------------------- Forces Calculation GPU acceleration : No Total electronic charge : 0.999999978668 Calculate local forces : Yes Calculate Non Local forces : No #-------------------------------------------------------------------- Timing for root process Timings for root process: CPU time (s) : 1.99 Elapsed time (s) : 1.02 BigDFT infocode : 0 Average noise forces: {x: 1.54474593E-05, y: 1.54474593E-05, z: 5.87062952E-07, total: 2.18538931E-05} Clean forces norm (Ha/Bohr): {maxval: 2.284167104466E-01, fnrm2: 1.043483872224E-01} Raw forces norm (Ha/Bohr): {maxval: 2.284171259842E-01, fnrm2: 1.043483877050E-01} #------------------------------------------------------------------------------ Atomic Forces Atomic Forces (Ha/Bohr): - {H: [ 2.117582368136E-22, 2.117582368136E-22, 2.284167104466E-01]} # 0001 - {H: [-2.117582368136E-22, -2.117582368136E-22, -2.284167104466E-01]} # 0002 Energy (Hartree) : -6.01595564725052157E-01 Force Norm (Hartree/Bohr) : 3.23030009786162475E-01 Wavefunction Optimization Finished, exit signal: 0 --- #----------------------------------------------------------- Geometry minimization using BFGS Begin of minimization using : BFGS #--------------------------------------------------------------------------- Input parameters DFT parameters: eXchange Correlation: XC ID : &ixc 1000 Exchange-Correlation reference : "No Hartree and XC terms" XC functional implementation : ABINIT Polarisation : 1 Spin polarization : collinear Net Charge (Ions-Electrons) : 1.00000 Basis set definition: Suggested Grid Spacings (a0) : [ 0.45, 0.45, 0.45 ] Coarse and Fine Radii Multipliers : [ 3.0, 7.0 ] Self-Consistent Cycle Parameters: Wavefunction: Gradient Norm Threshold : &gnrm_cv 1.0E-07 CG Steps for Preconditioner : 6 DIIS History length : 6 Max. Wfn Iterations : &itermax 100 Max. Subspace Diagonalizations : 1 Input wavefunction policy : INPUT_PSI_MEMORY_WVL # 1 Output wavefunction policy : NONE # 0 Output grid policy : NONE # 0 Virtual orbitals : 0 Number of plotted density orbitals: 0 Density/Potential: Max. Iterations : 1 Post Optimization Parameters: Finite-Size Effect estimation: Scheduled : No #-------------------------------------------------------------------------- System Properties Properties of atoms in the system: - Symbol : H #Type No. 01 No. of Electrons : 1 No. of Atoms : 2 Radii of active regions (AU): Coarse : 1.46342 Fine : 0.20000 Coarse PSP : 0.00000 Source : PSP File Grid Spacing threshold (AU) : 0.50 Pseudopotential type : HGH Local Pseudo Potential (HGH convention): Rloc : 0.20000 Coefficients (c1 .. c4) : [ -4.18024, 0.72508, 0.00000, 0.00000 ] No. of projectors : 0 PSP XC : "No Hartree and XC terms" #-------------------------------------------------- Atom Positions (specified and grid units) Atomic structure: Units : bohr Positions: - {H: [ 4.275000000, 4.275000000, 6.175000000], # [ 9.50, 9.50, 13.72 ] 0001 IGSpin: 1} - H: [ 4.275000000, 4.275000000, 4.175000000] # [ 9.50, 9.50, 9.28 ] 0002 Rigid Shift Applied (AU) : [ 4.2750, 4.2750, 5.1750 ] #---------------------------------------------------------------------------- Grid properties Box Grid spacings : [ 0.4500, 0.4500, 0.4500 ] Sizes of the simulation domain: AU : [ 8.5500, 8.5500, 10.350 ] Angstroem : [ 4.5245, 4.5245, 5.4770 ] Grid Spacing Units : [ 19, 19, 23 ] High resolution region boundaries (GU): From : [ 7, 7, 7 ] To : [ 12, 12, 16 ] High Res. box is treated separately : Yes Wavefunctions Descriptors, full simulation domain: Coarse resolution grid: No. of segments : 384 No. of points : 5176 Fine resolution grid: No. of segments : 56 No. of points : 248 #---------------------------------------------------------------------- Kernel Initialization Poisson Kernel Initialization: #------------------------------------------------------------------------- Input parameters kernel: screening : 0 # Mu screening parameter isf_order : 16 # Order of the Interpolating Scaling Function family stress_tensor : Yes # Triggers the calculation of the stress tensor environment: cavity : none # Type of the cavity fd_order : 16 # Order of the Finite-difference derivatives for the GPS solver itermax : 200 # Maximum number of iterations of the GPS outer loop minres : 1.e-8 # Convergence threshold of the loop pb_method : none # Defines the method for the Poisson Boltzmann Equation setup: accel : none # Material Acceleration taskgroup_size : 0 # Size of the taskgroups of the Poisson Solver global_data : No # Charge density and Electrostatic potential are given by global arrays verbose : Yes # Verbosity switch output : none # Quantities to be plotted after the main solver routine MPI tasks : 1 Poisson Kernel Creation: Boundary Conditions : Free Memory Requirements per MPI task: Density (MB) : 2.99 Kernel (MB) : 3.12 Full Grid Arrays (MB) : 2.80 #---------------------------------------------------------- Electronic Orbital Initialization Total Number of Electrons : 1 Spin treatment : Collinear Orbitals Repartition: MPI tasks 0- 0 : 1 Total Number of Orbitals : 1 Input Occupation Numbers: - Occupation Numbers: {Orbital No. 1: 1.0000} Wavefunctions memory occupation for root MPI process: 0 MB 54 KB 0 B NonLocal PSP Projectors Descriptors: Creation strategy : On-the-fly Total number of projectors : 0 Total number of components : 0 Percent of zero components : 0 Communication checks: Transpositions : Yes Reverse transpositions : Yes #----------------------------------------------------------- Estimation of Memory Consumption Memory requirements for principal quantities (MiB.KiB): Subspace Matrix : 0.1 # (Number of Orbitals: 1) Single orbital : 0.54 # (Number of Components: 6912) All (distributed) orbitals : 0.108 # (Number of Orbitals per MPI task: 1) Wavefunction storage size : 0.756 # (DIIS/SD workspaces included) Nonlocal Pseudopotential Arrays : 0.0 Full Uncompressed (ISF) grid : 5.609 Workspaces storage size : 0.169 Accumulated memory requirements during principal run stages (MiB.KiB): Kernel calculation : 34.275 Density Construction : 28.624 Poisson Solver : 51.723 Hamiltonian application : 28.727 Orbitals Orthonormalization : 28.727 Estimated Memory Peak (MB) : 51 Ion-Ion interaction energy : 5.00000000000000E-01 #------------------------------------------------------------------- Ionic Potential Creation Total ionic charge : -2.000000714589 Poisson Solver: BC : Free Box : [ 69, 69, 77 ] MPI tasks : 1 Interaction energy ions multipoles : 0.0 Interaction energy multipoles multipoles: 0.0 #---------------------------------------------------------------------- Wavefunctions Restart Input Hamiltonian: Reformating Wavefunctions : No #---------------------------------------------------------------------- Self-Consistent Cycle Ground State Optimization: - Hamiltonian Optimization: &itrp001 - Subspace Optimization: &itrep001-01 Wavefunctions Iterations: - { #------------------------------------------------------------------------- iter: 1 BIGDFT_RUNTIME_ERROR: {Id: 28, Message: An invalid operation has been done during runtime, Action: Check the exact unrolling of runtime operations, likely something has been initialized/finalized twice, }, Additional Info: psitohpsi: KS_potential not available, control the operations on rhov, #Error raised! #^^^^ Messages are above, dumping run status in file(s) bigdft-err-*.yaml of directory debug/ #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Exiting...