diff --git a/tests/data/parsers/bigdft/output.out b/tests/data/parsers/bigdft/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..0279db2fc876fd0bfed2cb6ba3c31246b4b4521c
--- /dev/null
+++ b/tests/data/parsers/bigdft/output.out
@@ -0,0 +1,707 @@
+---
+ 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
+ Timestamp of this run : 2016-11-11 13:02:23.583
+ Root process Hostname : lenovo700
+ Number of MPI tasks : 1
+ OpenMP parallelization : Yes
+ Maximal OpenMP threads per MPI task : 8
+ #------------------------------------------------------------------ Code compiling options
+ Compilation options:
+ Configure arguments:
+ " '--prefix' '/home/lauri/bigdft-suite/build/install' 'FC=mpif90' 'FCFLAGS=-O2
+ -fopenmp' 'CFLAGS=-O2 -fopenmp' 'LIBS=-llapack -lblas -ldl'
+ 'LDFLAGS=-L/home/lauri/bigdft-suite/build/install/lib '
+ 'C_INCLUDE_PATH=/home/lauri/bigdft-suite/build/install/include'
+ 'PKG_CONFIG_PATH=/home/lauri/bigdft-suite/build/install/lib/pkgconfig:/home/lauri/bigdft
+ -suite/build/install/share/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgcon
+ fig:/usr/share/pkgconfig'"
+ Compilers (CC, FC, CXX) : [ gcc, mpif90, g++ ]
+ Compiler flags:
+ CFLAGS : -O2 -fopenmp
+ FCFLAGS : -O2 -fopenmp
+ CXXFLAGS : -g -O2
+ #------------------------------------------------------------------------ Input parameters
+ radical : null
+ outdir : ./
+ logfile : No
+ run_from_files : Yes
+ 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
+ cavitation : Yes # Triggers the evaluation of the extra cavitation terms
+ gammaS : 72.0 # Cavitation term, surface tension of the solvent [dyn/cm]
+ alphaS : -22.0 # Proportionality of repulsion free energy in term of the surface integral [dyn/cm]
+ betaV : -0.35 # Proportionality of dispersion free energy in term of volume integral [GPa]
+ input_guess : Yes # Triggers the input guess procedure of gps_algorithm
+ fd_order : 16 # Order of the Finite-difference derivatives for the GPS solver
+ itermax : 50 # 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
+ dft:
+ hgrids: [0.45, 0.45, 0.45] # Grid spacing in the three directions (bohr)
+ rmult: [5., 8.] # c(f)rmult*radii_cf(:,1(2))=coarse(fine) atom-based radius
+ ixc : 1 # Exchange-correlation parameter (LDA=1,PBE=11)
+ qcharge : 0 # Charge of the system. Can be integer or real.
+ elecfield: [0., 0., 0.] # Electric field (Ex,Ey,Ez)
+ nspin : 1 # Spin polarization treatment
+ mpol : 0 # Total magnetic moment
+ gnrm_cv : 1.e-4 # convergence criterion gradient
+ itermax : 50 # Max. iterations of wfn. opt. steps
+ itermin : 0 # Minimal iterations of wfn. optimzed 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_wf : 0 # Output of the support functions
+ 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 virtual orbs
+ 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
+ disablesym : No # Disable the symmetry detection
+ external_potential:
+ values : __not_a_value__
+ 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
+ output:
+ atomic_density_matrix : None # Dictionary of the atoms for which the atomic density matrix has to be plotted
+ kpt:
+ method : manual # K-point sampling method
+ kpt: # Kpt coordinates
+ - [0., 0., 0.]
+ wkpt: [1.] # Kpt weights
+ bands : No # For doing band structure calculation
+ geopt:
+ method : none # Geometry optimisation method
+ ncount_cluster_x : 1 # Maximum number of force evaluations
+ frac_fluct : 1. # Fraction of force fluctuations. Stop if fmax < forces_fluct*frac_fluct
+ forcemax : 0. # Max forces criterion when stop
+ randdis : 0. # Random displacement amplitude
+ betax : 4. # Stepsize for the geometry optimization
+ beta_stretchx : 5e-1 # Stepsize for steepest descent in stretching mode direction (only if in biomode)
+ 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
+ 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 parameters
+ 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
+ perf:
+ debug : No # Debug option
+ profiling_depth : -1 # maximum level of the profiling for the tracking of the routines
+ 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
+ exctxpar : OP2P # Exact exchange parallelisation scheme
+ 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
+ verbosity : 2 # Verbosity of the output
+ 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
+ pdsyev_blocksize : -8 # SCALAPACK linear scaling blocksize
+ pdgemm_blocksize : -8 # SCALAPACK linear scaling blocksize
+ maxproc_pdsyev : 4 # SCALAPACK linear scaling max num procs
+ maxproc_pdgemm : 4 # SCALAPACK linear scaling max num procs
+ ef_interpol_det : 1.e-12 # FOE max determinant of cubic interpolation matrix
+ ef_interpol_chargediff : 1.0 # FOE max charge difference for interpolation
+ 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
+ write_orbitals : 0 # Linear scaling write KS orbitals for cubic restart (might take lot of disk space!)
+ 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)
+ evbounds_nsatur : 3 # Number of FOE cycles before the eigenvalue bounds are shrinked (linear)
+ evboundsshrink_nsatur : 4 # maximal number of unsuccessful eigenvalue bounds shrinkings
+ 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
+ fscale_lowerbound : 5.e-3 # linear scaling lower bound for the error function decay length
+ fscale_upperbound : 5.e-2 # linear scaling upper bound for the error function decay length
+ 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
+ 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)
+ 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
+ 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
+ eval_range_foe: [-0.5, 0.5] # Lower and upper bound of the eigenvalue spectrum, will be adjusted
+ # automatically if chosen unproperly
+ fscale_foe : 2.e-2 # decay length of the error function
+ coeff_scaling_factor : 1.0 # factor to scale the gradient in direct minimization
+ pexsi_npoles : 40 # number of poles used 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
+ 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
+ psppar.N:
+ Pseudopotential type : HGH-K
+ Atomic number : 7
+ No. of Electrons : 5
+ Pseudopotential XC : 1
+ Local Pseudo Potential (HGH convention):
+ Rloc : 0.28917923
+ Coefficients (c1 .. c4): [-12.23481988, 1.76640728, 0.0, 0.0]
+ NonLocal PSP Parameters:
+ - Channel (l) : 0
+ Rloc : 0.25660487
+ h_ij terms: [13.55224272, 0.0, 0.0, 0.0, 0.0, 0.0]
+ - Channel (l) : 1
+ Rloc : 0.27013369
+ h_ij terms: [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+ Source : Hard-Coded
+ Radii of active regions (AU):
+ Coarse : 1.370256482166319
+ Fine : 0.25660487
+ Coarse PSP : 0.50650066875
+ Source : Hard-Coded
+ posinp:
+ #---------------------------------------------- Atomic positions (by default bohr units)
+ units : angstroem
+ positions:
+ - N: [0.0, 0.0, 0.0]
+ - N: [0.0, 0.0, 1.114989995956421]
+ properties:
+ format : xyz
+ source : posinp.xyz
+ #--------------------------------------------------------------------------------------- |
+ Data Writing directory : ./
+ #-------------------------------------------------- Input Atomic System (file: posinp.xyz)
+ Atomic System Properties:
+ Number of atomic types : 1
+ Number of atoms : 2
+ Types of atoms : [ N ]
+ Boundary Conditions : Free #Code: F
+ Number of Symmetries : 0
+ Space group : disabled
+ #------------------------------ Geometry optimization Input Parameters (file: input.geopt)
+ Geometry Optimization Parameters:
+ Maximum steps : 1
+ Algorithm : none
+ Random atomic displacement : 0.0E+00
+ Fluctuation in forces : 1.0E+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 1
+ Exchange-Correlation reference : "XC: Teter 93"
+ XC functional implementation : ABINIT
+ Spin polarization : No
+ Basis set definition:
+ Suggested Grid Spacings (a0) : [ 0.45, 0.45, 0.45 ]
+ Coarse and Fine Radii Multipliers : [ 5.0, 8.0 ]
+ Self-Consistent Cycle Parameters:
+ Wavefunction:
+ Gradient Norm Threshold : &gnrm_cv 1.0E-04
+ CG Steps for Preconditioner : 6
+ DIIS History length : 6
+ Max. Wfn Iterations : &itermax 50
+ 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 : N #Type No. 01
+ No. of Electrons : 5
+ No. of Atoms : 2
+ Radii of active regions (AU):
+ Coarse : 1.37026
+ Fine : 0.25660
+ Coarse PSP : 0.50650
+ Source : Hard-Coded
+ Grid Spacing threshold (AU) : 0.64
+ Pseudopotential type : HGH-K
+ Local Pseudo Potential (HGH convention):
+ Rloc : 0.28918
+ Coefficients (c1 .. c4) : [ -12.23482, 1.76641, 0.00000, 0.00000 ]
+ NonLocal PSP Parameters:
+ - Channel (l) : 0
+ Rloc : 0.25660
+ h_ij matrix:
+ - [ 13.55224, 0.00000, 0.00000 ]
+ - [ 0.00000, 0.00000, 0.00000 ]
+ - [ 0.00000, 0.00000, 0.00000 ]
+ No. of projectors : 1
+ PSP XC : "XC: Teter 93"
+ #----------------------------------------------- Atom Positions (specified and grid units)
+ Atomic structure:
+ Units : angstroem
+ Positions:
+ - N: [ 3.571946174, 3.571946174, 3.609775538] # [ 15.00, 15.00, 15.16 ] 0001
+ - N: [ 3.571946174, 3.571946174, 4.724765534] # [ 15.00, 15.00, 19.84 ] 0002
+ Rigid Shift Applied (AU) : [ 6.7500, 6.7500, 6.8215 ]
+ #------------------------------------------------------------------------- Grid properties
+ Box Grid spacings : [ 0.4500, 0.4500, 0.4500 ]
+ Sizes of the simulation domain:
+ AU : [ 13.500, 13.500, 15.750 ]
+ Angstroem : [ 7.1439, 7.1439, 8.3345 ]
+ Grid Spacing Units : [ 30, 30, 35 ]
+ High resolution region boundaries (GU):
+ From : [ 11, 11, 11 ]
+ To : [ 19, 19, 24 ]
+ High Res. box is treated separately : Yes
+ #------------------------------------------------------------------- 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
+ cavitation : Yes # Triggers the evaluation of the extra cavitation terms
+ gammaS : 72.0 # Cavitation term, surface tension of the solvent [dyn/cm]
+ alphaS : -22.0 # Proportionality of repulsion free energy in term of the surface integral [dyn/cm]
+ betaV : -0.35 # Proportionality of dispersion free energy in term of volume integral [GPa]
+ input_guess : Yes # Triggers the input guess procedure of gps_algorithm
+ fd_order : 16 # Order of the Finite-difference derivatives for the GPS solver
+ itermax : 50 # 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
+ OpenMP threads per MPI task : 8
+ Poisson Kernel Creation:
+ Boundary Conditions : Free
+ Memory Requirements per MPI task:
+ Density (MB) : 7.38
+ Kernel (MB) : 7.61
+ Full Grid Arrays (MB) : 6.38
+ Wavefunctions Descriptors, full simulation domain:
+ Coarse resolution grid:
+ No. of segments : 876
+ No. of points : 18172
+ Fine resolution grid:
+ No. of segments : 110
+ No. of points : 702
+ #---------------------------------------------------------------------- Occupation Numbers
+ Total Number of Electrons : 10
+ Spin treatment : Averaged
+ Orbitals Repartition:
+ MPI tasks 0- 0 : 5
+ Total Number of Orbitals : 5
+ Input Occupation Numbers:
+ - Occupation Numbers: {Orbitals No. 1-5: 2.0000}
+ Wavefunctions memory occupation for root MPI process: 0 MB 901 KB 816 B
+ NonLocal PSP Projectors Descriptors:
+ Creation strategy : On-the-fly
+ Total number of projectors : 2
+ Total number of components : 5905
+ Percent of zero components : 14
+ Size of workspaces : 23636
+ Maximum size of masking arrays for a projector: 951
+ Cumulative size of masking arrays : 1902
+ 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: 5)
+ Single orbital : 0.181 # (Number of Components: 23086)
+ All (distributed) orbitals : 1.780 # (Number of Orbitals per MPI task: 5)
+ Wavefunction storage size : 12.338 # (DIIS/SD workspaces included)
+ Nonlocal Pseudopotential Arrays : 0.47
+ Full Uncompressed (ISF) grid : 6.391
+ Workspaces storage size : 0.477
+ Accumulated memory requirements during principal run stages (MiB.KiB):
+ Kernel calculation : 83.719
+ Density Construction : 51.909
+ Poisson Solver : 79.48
+ Hamiltonian application : 52.243
+ Orbitals Orthonormalization : 52.243
+ Estimated Memory Peak (MB) : 83
+ Ion-Ion interaction energy : 1.18650663422787E+01
+ #---------------------------------------------------------------- Ionic Potential Creation
+ Total ionic charge : -10.000000000000
+ Poisson Solver:
+ BC : Free
+ Box : [ 91, 91, 101 ]
+ 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 : 8
+ Atomic Input Orbital Generation:
+ - {Atom Type: N, Electronic configuration: {
+ s: [ 2.00],
+ p: [ 1.00, 1.00, 1.00]}}
+ Wavelet conversion succeeded : Yes
+ Deviation from normalization : 2.05E-05
+ GPU acceleration : No
+ Total electronic charge : 9.999998731141
+ Poisson Solver:
+ BC : Free
+ Box : [ 91, 91, 101 ]
+ MPI tasks : 1
+ Expected kinetic energy : 13.9048146790
+ Energies: {Ekin: 1.39077628900E+01, Epot: -2.18665699073E+01, Enl: 2.33310272888E+00,
+ EH: 2.73028082106E+01, EXC: -4.69901727500E+00, EvXC: -6.15435941415E+00}
+ EKS : -1.96081040175154442E+01
+ Input Guess Overlap Matrices: {Calculated: Yes, Diagonalized: Yes}
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.040786533967E+00, f: 2.0000}, # 00001
+ {e: -5.272089296364E-01, f: 2.0000}, # 00002
+ {e: -4.411025209214E-01, f: 2.0000}, # 00003
+ {e: -4.411012163712E-01, f: 2.0000}, # 00004
+ {e: -3.946499923151E-01, f: 2.0000}, # 00005
+ {e: -1.011703410493E-01, f: 0.0000}, # 00006
+ {e: -1.011696286352E-01, f: 0.0000}, # 00007
+ {e: 6.775799490560E-01, f: 0.0000}] # 00008
+ IG wavefunctions defined : Yes
+ Accuracy estimation for this run:
+ Energy : 2.95E-03
+ Convergence Criterion : 5.90E-04
+ #------------------------------------------------------------------- Self-Consistent Cycle
+ Ground State Optimization:
+ - Hamiltonian Optimization: &itrp001
+ - Subspace Optimization: &itrep001-01
+ Wavefunctions Iterations:
+ - { #---------------------------------------------------------------------- iter: 1
+ GPU acceleration: No, Total electronic charge: 9.999998907187,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.31555268971E+01, Epot: -2.15786908762E+01, Enl: 1.86116449489E+00,
+ EH: 2.63308588225E+01, EXC: -4.58275164847E+00, EvXC: -6.00085488206E+00},
+ iter: 1, EKS: -1.96096887307935432E+01, gnrm: 3.17E-01, D: -1.58E-03,
+ DIIS weights: [ 1.00E+00, 1.00E+00], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 2
+ GPU acceleration: No, Total electronic charge: 9.999998911635,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.44508411437E+01, Epot: -2.17197324334E+01, Enl: 1.88603924516E+00,
+ EH: 2.78363997504E+01, EXC: -4.81126269619E+00, EvXC: -6.30251508668E+00},
+ iter: 2, EKS: -1.98629330621171434E+01, gnrm: 1.01E-01, D: -2.53E-01,
+ DIIS weights: [-3.44E-02, 1.03E+00, -3.69E-03], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 3
+ GPU acceleration: No, Total electronic charge: 9.999998874101,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.44411869578E+01, Epot: -2.17469810499E+01, Enl: 1.75966471693E+00,
+ EH: 2.76796262320E+01, EXC: -4.77628572993E+00, EvXC: -6.25642597000E+00},
+ iter: 3, EKS: -1.98805490248799117E+01, gnrm: 4.16E-02, D: -1.76E-02,
+ DIIS weights: [-4.35E-02, -3.03E-01, 1.35E+00, -1.53E-04], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 4
+ GPU acceleration: No, Total electronic charge: 9.999998826002,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45294911882E+01, Epot: -2.18293843168E+01, Enl: 1.76650692353E+00,
+ EH: 2.76953336562E+01, EXC: -4.77679601676E+00, EvXC: -6.25714802956E+00},
+ iter: 4, EKS: -1.98833015062267933E+01, gnrm: 1.08E-02, D: -2.75E-03,
+ DIIS weights: [ 8.60E-03, 2.87E-03, -1.93E-01, 1.18E+00, -9.40E-06],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 5
+ GPU acceleration: No, Total electronic charge: 9.999998813322,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45429965684E+01, Epot: -2.18430956587E+01, Enl: 1.75560375950E+00,
+ EH: 2.76838108599E+01, EXC: -4.77502857050E+00, EvXC: -6.25481901477E+00},
+ iter: 5, EKS: -1.98834494042030414E+01, gnrm: 3.62E-03, D: -1.48E-04,
+ DIIS weights: [-2.13E-04, 2.09E-02, -6.57E-02, -2.13E-01, 1.26E+00, -9.07E-07],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 6
+ GPU acceleration: No, Total electronic charge: 9.999998809276,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45534057718E+01, Epot: -2.18517502440E+01, Enl: 1.75534551625E+00,
+ EH: 2.76854781867E+01, EXC: -4.77548415617E+00, EvXC: -6.25542157493E+00},
+ iter: 6, EKS: -1.98834733816428653E+01, gnrm: 1.79E-03, D: -2.40E-05,
+ DIIS weights: [-6.18E-04, -8.84E-03, 3.93E-02, -1.23E-02, -5.50E-01, 1.53E+00,
+ -1.56E-07], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 7
+ GPU acceleration: No, Total electronic charge: 9.999998808800,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45574354724E+01, Epot: -2.18545160038E+01, Enl: 1.75424344147E+00,
+ EH: 2.76856816500E+01, EXC: -4.77559071591E+00, EvXC: -6.25556259134E+00},
+ iter: 7, EKS: -1.98834805221821824E+01, gnrm: 9.80E-04, D: -7.14E-06,
+ DIIS weights: [ 6.35E-04, 2.49E-04, -1.39E-02, 1.30E-01, -7.02E-01, 1.59E+00,
+ -4.82E-08], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 8
+ GPU acceleration: No, Total electronic charge: 9.999998808955,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45585865976E+01, Epot: -2.18552611953E+01, Enl: 1.75369436303E+00,
+ EH: 2.76855477173E+01, EXC: -4.77561167104E+00, EvXC: -6.25559037882E+00},
+ iter: 8, EKS: -1.98834829018645678E+01, gnrm: 4.87E-04, D: -2.38E-06,
+ DIIS weights: [-1.25E-03, -2.64E-03, 1.22E-02, 1.50E-01, -1.11E+00, 1.95E+00,
+ -7.65E-09], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 9
+ GPU acceleration: No, Total electronic charge: 9.999998809025,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45591635735E+01, Epot: -2.18555567520E+01, Enl: 1.75332018231E+00,
+ EH: 2.76854604236E+01, EXC: -4.77562597888E+00, EvXC: -6.25560937964E+00},
+ iter: 9, EKS: -1.98834836767451435E+01, gnrm: 1.31E-04, D: -7.75E-07,
+ DIIS weights: [-1.64E-03, -9.38E-03, 7.64E-02, -3.50E-02, -4.11E-01, 1.38E+00,
+ -6.64E-10], Orthogonalization Method: 0}
+ - { #--------------------------------------------------------------------- iter: 10
+ GPU acceleration: No, Total electronic charge: 9.999998809003,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45591939430E+01, Epot: -2.18555654633E+01, Enl: 1.75324569292E+00,
+ EH: 2.76854068846E+01, EXC: -4.77562353252E+00, EvXC: -6.25560617828E+00},
+ iter: 10, EKS: -1.98834837239079647E+01, gnrm: 3.36E-05, D: -4.72E-08,
+ DIIS weights: [ 2.51E-03, -1.69E-02, 3.31E-02, 5.80E-02, -4.50E-01, 1.37E+00,
+ -6.80E-11], Orthogonalization Method: 0}
+ - &FINAL001 { #---------------------------------------------------------- iter: 11
+ GPU acceleration: No, Total electronic charge: 9.999998809000,
+ Poisson Solver: {BC: Free, Box: [ 91, 91, 101 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes,
+ iter: 11, EKS: -1.98834837256869790E+01, gnrm: 3.36E-05, D: -1.78E-09, #FINAL
+ Energies: {Ekin: 1.45591701402E+01, Epot: -2.18555508038E+01, Enl: 1.75324278714E+00,
+ EH: 2.76853941958E+01, EXC: -4.77562153507E+00, EvXC: -6.25560353939E+00,
+ Eion: 1.18650663423E+01},
+ }
+ Non-Hermiticity of Hamiltonian in the Subspace: 4.03E-31
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.031892602676E+00, f: 2.0000}, # 00001
+ {e: -4.970106443181E-01, f: 2.0000}, # 00002
+ {e: -4.307276296665E-01, f: 2.0000}, # 00003
+ {e: -4.307272896460E-01, f: 2.0000}, # 00004
+ {e: -3.812107719151E-01, f: 2.0000}] # 00005
+ Last Iteration : *FINAL001
+ #---------------------------------------------------------------------- Forces Calculation
+ GPU acceleration : No
+ Total electronic charge : 9.999998809000
+ Poisson Solver:
+ BC : Free
+ Box : [ 91, 91, 101 ]
+ MPI tasks : 1
+ Multipole analysis origin : [ 6.75E+00, 6.750000E+00, 7.875000E+00 ]
+ Electric Dipole Moment (AU):
+ P vector : [ -5.2306E-04, -5.2306E-04, -5.6277E-04 ]
+ norm(P) : 9.294589E-04
+ Electric Dipole Moment (Debye):
+ P vector : [ -1.3295E-03, -1.3295E-03, -1.4304E-03 ]
+ norm(P) : 2.362449E-03
+ Quadrupole Moment (AU):
+ Q matrix:
+ - [ 1.1003E+00, 1.2565E-04, 3.0382E-04]
+ - [ 1.2565E-04, 1.1003E+00, 3.0382E-04]
+ - [ 3.0382E-04, 3.0382E-04, -2.2005E+00]
+ trace : -1.83E-12
+ Calculate local forces : Yes
+ Calculate Non Local forces : Yes
+ #-------------------------------------------------------------------- Timing for root process
+ Timings for root process:
+ CPU time (s) : 21.41
+ Elapsed time (s) : 3.27
+ BigDFT infocode : 0
+ Average noise forces: {x: 1.13964092E-05, y: 1.13964092E-05, z: -1.80910187E-04,
+ total: 1.81626683E-04}
+ Clean forces norm (Ha/Bohr): {maxval: 5.670554140677E-02, fnrm2: 6.431036852471E-03}
+ Raw forces norm (Ha/Bohr): {maxval: 5.683346444573E-02, fnrm2: 6.431070377897E-03}
+ #------------------------------------------------------------------------------ Atomic Forces
+ Atomic Forces (Ha/Bohr):
+ - {N: [-1.694065894509E-21, -3.388131789017E-21, 5.670554140677E-02]} # 0001
+ - {N: [ 1.694065894509E-21, 3.388131789017E-21, -5.670554140677E-02]} # 0002
+ Energy (Hartree) : -1.98834837256869790E+01
+ Force Norm (Hartree/Bohr) : 8.01937457191684022E-02
+ Memory Consumption Report:
+ Tot. No. of Allocations : 3048
+ Tot. No. of Deallocations : 3048
+ Remaining Memory (B) : 0
+ Memory occupation:
+ Peak Value (MB) : 99.892
+ for the array : wz
+ in the routine : input_wf
+ Memory Peak of process : 123.180 MB
+ Walltime since initialization : 00:00:03.590597331
+ Max No. of dictionaries used : 4494 #( 1019 still in use)
+ Number of dictionary folders allocated: 1