diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..6da91049ab9cb8b07191fdbefb2dd19feb367c0f
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz
@@ -0,0 +1,7 @@
+ 2 angstroemd0 -1.98834837256869932E+01 (Ha) Geometry + metaData forces
+ free
+ N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
+ forces
+N -1.69406589450860068E-21 -1.69406589450860068E-21 5.67055414067696439E-02
+N 1.69406589450860068E-21 1.69406589450860068E-21 -5.67055414067696439E-02
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f468acac1a41b1bef200c71027b601610a130937
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml
@@ -0,0 +1,16 @@
+ #---------------------------------------------------------------------- Minimal input file
+ #This file indicates the minimal set of input variables which has to be given to perform
+ #the run. The code would produce the same output if this file is used as input.
+ posinp:
+ units: angstroem
+ positions:
+ - N: [0.0, 0.0, 0.0]
+ - N: [0.0, 0.0, 1.114989995956421]
+ properties:
+ format: xyz
+ source: posinp.xyz
+ psolver:
+ environment:
+ gammaS: water
+ alphaS: water
+ betaV: water
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/output.out b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..88bf0bbb2a1efec67688a873493a4117eef0c445
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/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 : 2016-12-02 08:53:38.687
+ 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: -1.96096887307935148E+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: -1.98629330621171292E+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: -1.98805490248799472E+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: -1.98833015062267791E+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: -1.98834494042030343E+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: -1.98834733816428582E+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: -1.98834829018645323E+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: -1.98834836767451648E+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: -1.98834837256869932E+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: 3.24E-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 : -1.82E-12
+ Calculate local forces : Yes
+ Calculate Non Local forces : Yes
+ #-------------------------------------------------------------------- Timing for root process
+ Timings for root process:
+ CPU time (s) : 20.91
+ Elapsed time (s) : 3.18
+ 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: 6.431036852470E-03}
+ Raw forces norm (Ha/Bohr): {maxval: 5.683346444573E-02, fnrm2: 6.431070377896E-03}
+ #------------------------------------------------------------------------------ Atomic Forces
+ Atomic Forces (Ha/Bohr):
+ - {N: [-1.694065894509E-21, -1.694065894509E-21, 5.670554140677E-02]} # 0001
+ - {N: [ 1.694065894509E-21, 1.694065894509E-21, -5.670554140677E-02]} # 0002
+ Energy (Hartree) : -1.98834837256869932E+01
+ Force Norm (Hartree/Bohr) : 8.01937457191627401E-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 : 121.028 MB
+ Walltime since initialization : 00:00:03.945833943
+ Max No. of dictionaries used : 4494 #( 1019 still in use)
+ Number of dictionary folders allocated: 1
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..8d7121b05ee67690f5bc0c1b1acc2308488e51ef
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/posinp.xyz
@@ -0,0 +1,4 @@
+2 angstroem
+free
+N 0. 0. 0.
+N 0. 0. 1.11499
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/time.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/time.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..b7c056649121bc17b8e6f6d281d15179b307312d
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/time.yaml
@@ -0,0 +1,442 @@
+---
+ INIT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 10.9, 6.84E-02]
+ Communications : [ 0.0, 2.15E-05]
+ BLAS-LAPACK : [ 0.8, 5.05E-03]
+ PS Computation : [ 36.6, 0.23]
+ Potential : [ 6.7, 4.25E-02]
+ Convolutions : [ 12.4, 7.83E-02]
+ Other : [ 0.2, 1.21E-03]
+ Initialization : [ 5.0, 3.12E-02]
+ Total : [ 72.5, 0.63]
+ Categories: #Ordered by time consumption
+ PSolver Kernel Creation:
+ Data : [ 19.2, 0.12]
+ Class : PS Computation
+ Info : ISF operations and creation of the kernel
+ PSolver Computation:
+ Data : [ 17.4, 0.11]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Init to Zero:
+ Data : [ 7.1, 4.49E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ ApplyLocPotKin:
+ Data : [ 7.1, 4.48E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Exchange-Correlation:
+ Data : [ 6.7, 4.25E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ Rho_comput:
+ Data : [ 5.3, 3.35E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ wavefunction:
+ Data : [ 4.2, 2.63E-02]
+ Class : Initialization
+ Info : Miscellaneous
+ Array allocations:
+ Data : [ 2.4, 1.51E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.8, 5.05E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Routine Profiling:
+ Data : [ 0.7, 4.26E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Vector copy:
+ Data : [ 0.7, 4.15E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ CrtLocPot:
+ Data : [ 0.3, 2.20E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ Input_comput:
+ Data : [ 0.2, 1.45E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ CrtDescriptors:
+ Data : [ 0.2, 1.27E-03]
+ Class : Initialization
+ Info : RMA Pattern
+ ApplyProj:
+ Data : [ 0.1, 7.44E-04]
+ Class : Other
+ Info : RMA pattern
+ ionic_energy:
+ Data : [ 0.1, 3.89E-04]
+ Class : Other
+ Info : Miscellaneous
+ calc_bounds:
+ Data : [ 0.0, 3.91E-05]
+ Class : Other
+ Info : Miscellaneous
+ Un-TransSwitch:
+ Data : [ 0.0, 2.96E-05]
+ Class : Other
+ Info : RMA pattern
+ Allreduce, Large Size:
+ Data : [ 0.0, 1.38E-05]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ Pot_after_comm:
+ Data : [ 0.0, 7.87E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.96E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Small Size:
+ Data : [ 0.0, 1.67E-06]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ WFN_OPT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 17.7, 0.39]
+ Communications : [ 0.0, 5.29E-05]
+ BLAS-LAPACK : [ 0.4, 9.37E-03]
+ PS Computation : [ 18.1, 0.40]
+ Potential : [ 17.5, 0.39]
+ Convolutions : [ 33.7, 0.75]
+ Linear Algebra : [ 0.4, 8.93E-03]
+ Other : [ 9.9, 0.22]
+ Total : [ 97.8, 2.2]
+ Categories: #Ordered by time consumption
+ PSolver Computation:
+ Data : [ 18.1, 0.40]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Exchange-Correlation:
+ Data : [ 17.5, 0.39]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ ApplyLocPotKin:
+ Data : [ 13.5, 0.30]
+ Class : Convolutions
+ Info : OpenCL ported
+ Rho_comput:
+ Data : [ 10.9, 0.24]
+ Class : Convolutions
+ Info : OpenCL ported
+ Init to Zero:
+ Data : [ 10.3, 0.23]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Precondition:
+ Data : [ 9.3, 0.21]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyProj:
+ Data : [ 8.9, 0.20]
+ Class : Other
+ Info : RMA pattern
+ Array allocations:
+ Data : [ 2.8, 6.12E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Routine Profiling:
+ Data : [ 2.5, 5.55E-02]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Vector copy:
+ Data : [ 2.2, 4.82E-02]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Diis:
+ Data : [ 1.0, 2.21E-02]
+ Class : Other
+ Info : Other
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.4, 9.37E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Chol_comput:
+ Data : [ 0.4, 8.81E-03]
+ Class : Linear Algebra
+ Info : ALLReduce orbs
+ Un-TransSwitch:
+ Data : [ 0.0, 2.54E-04]
+ Class : Other
+ Info : RMA pattern
+ LagrM_comput:
+ Data : [ 0.0, 1.21E-04]
+ Class : Linear Algebra
+ Info : DGEMM
+ Pot_after_comm:
+ Data : [ 0.0, 8.37E-05]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.29E-05]
+ Class : Communications
+ Info : AllGathrv grid
+ LAST: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 15.4, 5.02E-02]
+ Communications : [ 0.0, 1.38E-05]
+ BLAS-LAPACK : [ 0.3, 1.01E-03]
+ PS Computation : [ 25.0, 8.17E-02]
+ Potential : [ 11.7, 3.83E-02]
+ Convolutions : [ 25.7, 8.40E-02]
+ Other : [ 8.0, 2.62E-02]
+ Finalization : [ 0.8, 2.69E-03]
+ Total : [ 87.0, 0.33]
+ Categories: #Ordered by time consumption
+ PSolver Computation:
+ Data : [ 25.0, 8.17E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Rho_comput:
+ Data : [ 14.6, 4.78E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Exchange-Correlation:
+ Data : [ 11.7, 3.83E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ ApplyLocPotKin:
+ Data : [ 11.1, 3.61E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Init to Zero:
+ Data : [ 10.4, 3.40E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ ApplyProj:
+ Data : [ 8.0, 2.62E-02]
+ Class : Other
+ Info : RMA pattern
+ Vector copy:
+ Data : [ 2.8, 9.08E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Array allocations:
+ Data : [ 1.2, 4.05E-03]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Routine Profiling:
+ Data : [ 0.9, 3.06E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Forces:
+ Data : [ 0.8, 2.69E-03]
+ Class : Finalization
+ Info : Miscellaneous
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.3, 9.85E-04]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Lapack (dsy-ssy-che-zhe)eev:
+ Data : [ 0.0, 3.00E-05]
+ Class : BLAS-LAPACK
+ Info : Lapack Eigenvalue Problem
+ Un-TransSwitch:
+ Data : [ 0.0, 1.22E-05]
+ Class : Other
+ Info : RMA pattern
+ Pot_after_comm:
+ Data : [ 0.0, 7.15E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.48E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Small Size:
+ Data : [ 0.0, 5.25E-06]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ Allreduce, Large Size:
+ Data : [ 0.0, 3.10E-06]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ SUMMARY: # % , Time (s)
+ INIT : [ 19.9, 0.63]
+ WFN_OPT : [ 69.8, 2.2]
+ LAST : [ 10.3, 0.33]
+ Total : [ 100.0, 3.2]
+ Routines timing and number of calls:
+ - Main_program: [ 3.93, 1, ~*]
+ Subroutines:
+ - process_run (id="posinp"): [ 3.18, 1, 80.83%*]
+ Subroutines:
+ - bigdft_state: [ 3.18, 1, 99.90%*]
+ Subroutines:
+ - quantum_mechanical_state: [ 3.17, 1, 99.76%*]
+ Subroutines:
+ - cluster: [ 3.17, 1, 100.03%]
+ Subroutines:
+ - Electrostatic_Solver: [ 0.629, 11, 19.85%]
+ Subroutines:
+ - apply_kernel: [ 0.605, 11, 96.13%]
+ Subroutines:
+ - G_PoissonSolver: [ 0.420, 11, 69.37%]
+ - XC_potential: [ 0.440, 11, 13.88%]
+ Subroutines:
+ - xc_energy_new: [ 0.416, 11, 94.65%]
+ Subroutines:
+ - xc_getvxc: [ 0.393, 11, 94.49%]
+ - LocalHamiltonianApplication: [ 0.401, 11, 12.65%]
+ Subroutines:
+ - psir_to_vpsi: [ 8.427E-02, 55, 21.02%]
+ Subroutines:
+ - apply_potential_lr_bounds: [ 8.006E-02, 55, 95.00%]
+ - orbital_basis_associate: [ 7.374E-04, 11, 0.18%]
+ - input_wf: [ 0.400, 1, 12.62%]
+ Subroutines:
+ - updatePotential: [ 9.890E-02, 1, 24.73%]
+ Subroutines:
+ - Electrostatic_Solver: [ 5.146E-02, 1, 52.04%]
+ Subroutines:
+ - apply_kernel: [ 4.950E-02, 1, 96.18%]
+ Subroutines:
+ - G_PoissonSolver: [ 4.089E-02, 1, 82.61%]
+ - XC_potential: [ 4.481E-02, 1, 45.30%]
+ Subroutines:
+ - xc_energy_new: [ 4.171E-02, 1, 93.08%]
+ Subroutines:
+ - xc_getvxc: [ 3.893E-02, 1, 93.32%]
+ - LocalHamiltonianApplication: [ 4.885E-02, 1, 12.21%]
+ Subroutines:
+ - psir_to_vpsi: [ 1.043E-02, 8, 21.35%]
+ Subroutines:
+ - apply_potential_lr_bounds: [ 9.872E-03, 8, 94.65%]
+ - orbital_basis_associate: [ 7.438E-05, 1, 0.15%]
+ - daub_to_isf: [ 2.496E-02, 8, 6.24%]
+ - LDiagHam: [ 6.851E-03, 1, 1.71%]
+ - check_linear_and_create_Lzd: [ 1.257E-03, 1, 0.31%]
+ - NonLocalHamiltonianApplication: [ 1.087E-03, 1, 0.27%]
+ Subroutines:
+ - atom_projector: [ 4.037E-04, 2, 37.14%]
+ Subroutines:
+ - crtproj: [ 3.028E-04, 2, 75.01%]
+ - orbital_basis_associate: [ 7.897E-05, 1, 7.27%]
+ - local_potential_dimensions: [ 2.057E-04, 3, 0.05%]
+ - deallocate_work_arrays_sumrho: [ 1.086E-04, 1, 0.03%]
+ - initialize_work_arrays_sumrho: [ 8.927E-05, 1, 0.02%]
+ - full_local_potential: [ 6.645E-05, 1, 0.02%]
+ - SynchronizeHamiltonianApplication: [ 1.804E-05, 1, 0.00%]
+ - preconditionall2: [ 0.298, 10, 9.41%]
+ Subroutines:
+ - precondition_preconditioner: [ 8.735E-02, 50, 29.31%]
+ Subroutines:
+ - prec_diag: [ 8.165E-02, 50, 93.48%]
+ - calculate_rmr_new: [ 2.798E-02, 300, 9.39%]
+ - compress_forstandard: [ 1.280E-02, 350, 4.29%]
+ - finalise_precond_residue: [ 1.502E-03, 50, 0.50%]
+ - NonLocalHamiltonianApplication: [ 0.244, 11, 7.70%]
+ Subroutines:
+ - atom_projector: [ 0.203, 22, 83.21%]
+ Subroutines:
+ - crtproj: [ 0.200, 22, 98.38%]
+ - orbital_basis_associate: [ 7.821E-04, 11, 0.32%]
+ - daub_to_isf: [ 0.158, 55, 4.97%]
+ - system_initialization: [ 0.152, 1, 4.79%]
+ Subroutines:
+ - pkernel_set: [ 0.130, 1, 85.60%]
+ Subroutines:
+ - mpi_environment_set: [ 1.627E-05, 1, 0.01%]
+ - createWavefunctionsDescriptors: [ 2.176E-03, 1, 1.43%]
+ Subroutines:
+ - fill_logrid: [ 1.882E-04, 2, 8.65%]
+ - segkeys: [ 1.310E-04, 2, 6.02%]
+ - num_segkeys: [ 6.667E-05, 2, 3.06%]
+ - createProjectorsArrays: [ 1.970E-03, 1, 1.30%]
+ Subroutines:
+ - localize_projectors: [ 3.041E-04, 1, 15.44%]
+ Subroutines:
+ - fill_logrid: [ 1.101E-04, 4, 36.21%]
+ - num_segkeys: [ 8.109E-05, 4, 26.66%]
+ - set_wfd_to_wfd: [ 1.631E-04, 2, 8.28%]
+ Subroutines:
+ - init_tolr: [ 9.121E-05, 2, 55.92%]
+ - fill_logrid: [ 1.066E-04, 4, 5.41%]
+ - segkeys: [ 9.551E-05, 4, 4.85%]
+ - transform_keyglob_to_keygloc: [ 8.327E-05, 4, 4.23%]
+ - allocate_arrays: [ 8.077E-05, 1, 4.10%]
+ - gaussian_basis_from_psp: [ 3.932E-05, 1, 2.00%]
+ - nullify_structure: [ 1.577E-05, 1, 0.80%]
+ - orbital_basis_associate: [ 7.075E-05, 1, 0.05%]
+ - mpi_environment_set: [ 2.706E-05, 1, 0.02%]
+ - kswfn_post_treatments: [ 0.117, 1, 3.68%]
+ Subroutines:
+ - Electrostatic_Solver: [ 4.524E-02, 1, 38.67%]
+ Subroutines:
+ - apply_kernel: [ 4.347E-02, 1, 96.09%]
+ Subroutines:
+ - G_PoissonSolver: [ 4.070E-02, 1, 93.64%]
+ - calculate_dipole_moment: [ 3.421E-02, 1, 29.24%]
+ - daub_to_isf: [ 1.492E-02, 5, 12.75%]
+ - calculate_forces: [ 3.409E-03, 1, 2.91%]
+ Subroutines:
+ - nonlocal_forces: [ 1.813E-03, 1, 53.17%]
+ Subroutines:
+ - atom_projector: [ 1.313E-03, 8, 72.43%]
+ Subroutines:
+ - crtproj: [ 1.029E-03, 8, 78.41%]
+ - local_forces: [ 1.481E-03, 1, 43.43%]
+ - rhocore_forces: [ 1.499E-05, 1, 0.44%]
+ - deallocate_work_arrays_sumrho: [ 1.051E-04, 1, 0.09%]
+ - initialize_work_arrays_sumrho: [ 9.186E-05, 1, 0.08%]
+ - orbital_basis_associate: [ 8.129E-05, 1, 0.07%]
+ - createEffectiveIonicPotential: [ 7.749E-02, 1, 2.44%]
+ Subroutines:
+ - createIonicPotential: [ 7.745E-02, 1, 99.94%]
+ Subroutines:
+ - Electrostatic_Solver: [ 6.985E-02, 1, 90.18%]
+ Subroutines:
+ - apply_kernel: [ 6.825E-02, 1, 97.71%]
+ Subroutines:
+ - G_PoissonSolver: [ 6.418E-02, 1, 94.04%]
+ - timing_dump_results: [ 1.666E-03, 2, 0.05%]
+ - deallocate_work_arrays_sumrho: [ 1.243E-03, 11, 0.04%]
+ - initialize_work_arrays_sumrho: [ 1.158E-03, 11, 0.04%]
+ - full_local_potential: [ 8.629E-04, 11, 0.03%]
+ - IonicEnergyandForces: [ 5.133E-04, 1, 0.02%]
+ Subroutines:
+ - vdwcorrection_calculate_energy: [ 2.188E-05, 1, 4.26%]
+ - vdwcorrection_calculate_forces: [ 1.581E-05, 1, 3.08%]
+ - SynchronizeHamiltonianApplication: [ 2.722E-04, 11, 0.01%]
+ - interaction_multipoles_ions: [ 1.312E-04, 1, 0.00%]
+ - ionic_energy_of_external_charges: [ 5.234E-05, 1, 0.00%]
+ - potential_from_charge_multipoles: [ 1.835E-05, 1, 0.00%]
+ - timing_dump_results: [ 7.660E-04, 1, 0.02%]
+ - bigdft_init: [ 0.713, 1, 18.13%]
+ Subroutines:
+ - mpi_environment_set: [ 7.590E-05, 1, 0.01%]
+ - run_objects_init: [ 4.323E-02, 1, 1.10%]
+ Subroutines:
+ - set_run_objects: [ 2.204E-02, 1, 50.98%]
+ Subroutines:
+ - inputs_from_dict: [ 2.197E-02, 1, 99.68%]
+ Subroutines:
+ - input_keys_fill_all: [ 9.360E-03, 1, 42.61%]
+ Subroutines:
+ - input_keys_init: [ 5.172E-03, 1, 55.26%]
+ - PS_input_dict: [ 8.858E-04, 1, 9.46%]
+ - input_keys_dump: [ 5.086E-03, 1, 23.15%]
+ - atomic_data_set_from_dict: [ 3.365E-03, 1, 15.32%]
+ - psp_dict_fill_all: [ 9.859E-04, 1, 4.49%]
+ - astruct_set_from_dict: [ 4.273E-04, 1, 1.94%]
+ - psp_dict_analyse: [ 2.290E-04, 1, 1.04%]
+ - allocateBasicArraysInputLin: [ 7.826E-05, 1, 0.36%]
+ - kpt_input_analyse: [ 4.855E-05, 1, 0.22%]
+ - atomic_gamma_from_dict: [ 2.668E-05, 1, 0.12%]
+ - occupation_set_from_dict: [ 2.611E-05, 1, 0.12%]
+ - input_analyze: [ 1.795E-05, 1, 0.08%]
+ - read_n_orbitals: [ 1.721E-05, 1, 0.08%]
+ - astruct_file_merge_to_dict: [ 1.736E-02, 1, 40.16%]
+ - read_input_dict_from_files: [ 1.218E-04, 1, 0.28%]
+ CPU parallelism:
+ MPI tasks : 1
+ OMP threads : 8
+ Report timestamp : 2016-12-02 08:53:41.913
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/forces_posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/forces_posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..1960e4db8fee92b74413deb0d6f55d5722787dc3
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/forces_posinp.xyz
@@ -0,0 +1,7 @@
+ 2 angstroemd0 -1.98842958295531673E+01 (Ha) Geometry + metaData forces
+periodic 7.00000000000000000E+00 7.00000000000000000E+00 7.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
+ forces
+N 0.00000000000000000E+00 0.00000000000000000E+00 5.62611962577510491E-02
+N 0.00000000000000000E+00 0.00000000000000000E+00 -5.62611962577510630E-02
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/input_minimal.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/input_minimal.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..d2960a7e31d3572095258fc786b92c9c0f6b81d4
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/input_minimal.yaml
@@ -0,0 +1,17 @@
+ #---------------------------------------------------------------------- Minimal input file
+ #This file indicates the minimal set of input variables which has to be given to perform
+ #the run. The code would produce the same output if this file is used as input.
+ posinp:
+ units: angstroem
+ cell: [ 7.0, 7.0, 7.0]
+ positions:
+ - N: [0.0, 0.0, 0.0]
+ - N: [0.0, 0.0, 1.114989995956421]
+ properties:
+ format: xyz
+ source: posinp.xyz
+ psolver:
+ environment:
+ gammaS: water
+ alphaS: water
+ betaV: water
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/output.out b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..ac854de1501e2dd6ad0c2b4885ed88b0a68b59ee
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/output.out
@@ -0,0 +1,730 @@
+---
+ 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 : 2016-12-02 09:05:18.705
+ 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
+ cell: [ 7.0, 7.0, 7.0]
+ 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 : Periodic #Code: P
+ Box Sizes (AU) : [ 1.32281E+01, 1.32281E+01, 1.32281E+01 ]
+ Number of Symmetries : 16
+ Space group : P 4/m m m
+ #------------------------------ 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
+ #------------------- K points description (Reduced and Brillouin zone coordinates, Weight)
+ K points:
+ - {Rc: [ 0.0000, 0.0000, 0.0000 ], Bz: [ 0.0000, 0.0000, 0.0000 ], Wgt: 1.0000} # 0001
+ 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
+ #----------------------------------------------------------------------- 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
+ Cell : [ 7.0, 7.0, 7.0 ]
+ Positions:
+ - N: [ 0.000000000, 0.000000000, 0.000000000] # [ 0.00, 0.00, 0.00 ] 0001
+ - N: [ 0.000000000, 0.000000000, 1.114989996] # [ 0.00, 0.00, 4.78 ] 0002
+ Rigid Shift Applied (AU) : [ -0.0000, -0.0000, -0.0000 ]
+ #------------------------------------------------------------------------- Grid properties
+ Box Grid spacings : [ 0.4409, 0.4409, 0.4409 ]
+ Sizes of the simulation domain:
+ AU : [ 13.228, 13.228, 13.228 ]
+ Angstroem : [ 7.0000, 7.0000, 7.0000 ]
+ Grid Spacing Units : [ 29, 29, 29 ]
+ High resolution region boundaries (GU):
+ From : [ 0, 0, 0 ]
+ To : [ 29, 29, 29 ]
+ High Res. box is treated separately : No
+ #------------------------------------------------------------------- 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 : Periodic
+ Memory Requirements per MPI task:
+ Density (MB) : 1.65
+ Kernel (MB) : 0.23
+ Full Grid Arrays (MB) : 1.65
+ #WARNING: The coarse grid does not fill the entire periodic box
+ #Errors due to translational invariance breaking may occur
+ Wavefunctions Descriptors, full simulation domain:
+ Coarse resolution grid:
+ No. of segments : 1552
+ No. of points : 18320
+ Fine resolution grid:
+ No. of segments : 222
+ No. of points : 742
+ #---------------------------------------------------------------------- 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:
+ #Kpt #0001 BZ coord. = [ 0.000000, 0.000000, 0.000000 ]
+ - Occupation Numbers: {Orbitals No. 1-5: 2.0000}
+ Wavefunctions memory occupation for root MPI process: 0 MB 918 KB 528 B
+ NonLocal PSP Projectors Descriptors:
+ Creation strategy : On-the-fly
+ Total number of projectors : 2
+ Total number of components : 6298
+ Percent of zero components : 14
+ Size of workspaces : 25208
+ Maximum size of masking arrays for a projector: 1980
+ Cumulative size of masking arrays : 3960
+ 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 : 0.184 # (Number of Components: 23514)
+ All (distributed) orbitals : 1.814 # (Number of Orbitals per MPI task: 5)
+ Wavefunction storage size : 12.572 # (DIIS/SD workspaces included)
+ Nonlocal Pseudopotential Arrays : 0.50
+ Full Uncompressed (ISF) grid : 1.664
+ Workspaces storage size : 0.422
+ Accumulated memory requirements during principal run stages (MiB.KiB):
+ Kernel calculation : 2.513
+ Density Construction : 21.75
+ Poisson Solver : 26.18
+ Hamiltonian application : 22.739
+ Orbitals Orthonormalization : 22.739
+ Estimated Memory Peak (MB) : 26
+ Ion-Ion interaction energy : 1.24464741081112E+00
+ #---------------------------------------------------------------- Ionic Potential Creation
+ Total ionic charge : -10.000000000000
+ Poisson Solver:
+ BC : Periodic
+ Box : [ 60, 60, 60 ]
+ 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 : 8.27E-05
+ GPU acceleration : No
+ Total electronic charge : 10.000108688102
+ Poisson Solver:
+ BC : Periodic
+ Box : [ 60, 60, 60 ]
+ MPI tasks : 1
+ Energies: {Ekin: 1.39082914713E+01, Epot: -2.16464328904E+01, Enl: 2.33300692222E+00,
+ EH: 1.69037290061E+01, EXC: -4.69922580474E+00, EvXC: -6.15463313317E+00}
+ EKS : -1.96088087637345616E+01
+ Input Guess Overlap Matrices: {Calculated: Yes, Diagonalized: Yes}
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.018637080551E+00, f: 2.0000}, # 00001
+ {e: -5.051392511972E-01, f: 2.0000}, # 00002
+ {e: -4.190691105582E-01, f: 2.0000}, # 00003
+ {e: -4.190675890907E-01, f: 2.0000}, # 00004
+ {e: -3.727120217116E-01, f: 2.0000}, # 00005
+ {e: -7.917083534872E-02, f: 0.0000}, # 00006
+ {e: -7.917005520217E-02, f: 0.0000}, # 00007
+ {e: 7.005074703646E-01, f: 0.0000}] # 00008
+ IG wavefunctions defined : Yes
+ #------------------------------------------------------------------- Self-Consistent Cycle
+ Ground State Optimization:
+ - Hamiltonian Optimization: &itrp001
+ - Subspace Optimization: &itrep001-01
+ Wavefunctions Iterations:
+ - { #---------------------------------------------------------------------- iter: 1
+ GPU acceleration: No, Total electronic charge: 10.000389750991,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.31541024170E+01, Epot: -2.13300849254E+01, Enl: 1.86120107969E+00,
+ EH: 1.59581966845E+01, EXC: -4.58252612643E+00, EvXC: -6.00055667889E+00},
+ iter: 1, EKS: -1.96103001499933249E+01, gnrm: 3.17E-01, D: -1.49E-03,
+ DIIS weights: [ 1.00E+00, 1.00E+00], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 2
+ GPU acceleration: No, Total electronic charge: 10.000299182451,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.49500192564E+01, Epot: -2.15440052080E+01, Enl: 1.91065086750E+00,
+ EH: 1.79217165021E+01, EXC: -4.89040031810E+00, EvXC: -6.40694209556E+00},
+ iter: 2, EKS: -1.98438623979024129E+01, gnrm: 1.02E-01, D: -2.34E-01,
+ DIIS weights: [ 3.47E-01, 6.53E-01, -1.42E-02], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 3
+ GPU acceleration: No, Total electronic charge: 10.000204591885,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.43177417128E+01, Epot: -2.15250349629E+01, Enl: 1.76258960286E+00,
+ EH: 1.71527215039E+01, EXC: -4.75189129400E+00, EvXC: -6.22430161725E+00},
+ iter: 3, EKS: -1.98803674170900422E+01, gnrm: 5.02E-02, D: -3.65E-02,
+ DIIS weights: [ 6.77E-02, 1.70E-01, 7.62E-01, -9.74E-04], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 4
+ GPU acceleration: No, Total electronic charge: 10.000220766542,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45137185665E+01, Epot: -2.15831215565E+01, Enl: 1.77024540614E+00,
+ EH: 1.73106246954E+01, EXC: -4.78099590172E+00, EvXC: -6.26267091351E+00},
+ iter: 4, EKS: -1.98834598567033893E+01, gnrm: 2.61E-02, D: -3.09E-03,
+ DIIS weights: [-1.13E-02, -2.67E-02, 2.03E-01, 8.35E-01, -9.78E-05],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 5
+ GPU acceleration: No, Total electronic charge: 10.000205386593,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45242139697E+01, Epot: -2.16145195007E+01, Enl: 1.75966413346E+00,
+ EH: 1.72778167566E+01, EXC: -4.77462231251E+00, EvXC: -6.25428545518E+00},
+ iter: 5, EKS: -1.98841476007647167E+01, gnrm: 1.14E-02, D: -6.88E-04,
+ DIIS weights: [-8.00E-03, -2.19E-02, -5.36E-02, 1.65E-01, 9.18E-01, -8.27E-06],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 6
+ GPU acceleration: No, Total electronic charge: 10.000203676683,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45448633546E+01, Epot: -2.16300485058E+01, Enl: 1.75612755724E+00,
+ EH: 1.72795953436E+01, EXC: -4.77485265716E+00, EvXC: -6.25459158576E+00},
+ iter: 6, EKS: -1.98842665980625846E+01, gnrm: 4.27E-03, D: -1.19E-04,
+ DIIS weights: [ 1.12E-03, 7.25E-03, -1.69E-02, -8.28E-02, 4.32E-02, 1.05E+00,
+ -8.99E-07], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 7
+ GPU acceleration: No, Total electronic charge: 10.000204908687,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45537287619E+01, Epot: -2.16361252066E+01, Enl: 1.75510640062E+00,
+ EH: 1.72814981072E+01, EXC: -4.77521363112E+00, EvXC: -6.25506783177E+00},
+ iter: 7, EKS: -1.98842865398945357E+01, gnrm: 1.81E-03, D: -1.99E-05,
+ DIIS weights: [ 5.03E-04, -1.40E-03, -1.48E-02, -5.24E-02, 6.95E-02, 9.99E-01,
+ -2.93E-07], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 8
+ GPU acceleration: No, Total electronic charge: 10.000205963000,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45569101867E+01, Epot: -2.16386676880E+01, Enl: 1.75456876300E+00,
+ EH: 1.72816257053E+01, EXC: -4.77527859396E+00, EvXC: -6.25515405451E+00},
+ iter: 8, EKS: -1.98842915721743374E+01, gnrm: 1.12E-03, D: -5.03E-06,
+ DIIS weights: [ 3.94E-03, 6.83E-03, -3.38E-02, -1.64E-01, -8.60E-03, 1.20E+00,
+ -9.85E-08], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 9
+ GPU acceleration: No, Total electronic charge: 10.000206948045,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45583505268E+01, Epot: -2.16398832182E+01, Enl: 1.75401539351E+00,
+ EH: 1.72812932424E+01, EXC: -4.77525741369E+00, EvXC: -6.25512622748E+00},
+ iter: 9, EKS: -1.98842943156039631E+01, gnrm: 7.00E-04, D: -2.74E-06,
+ DIIS weights: [ 4.16E-03, 2.35E-02, -2.51E-02, -3.51E-01, -1.99E-01, 1.55E+00,
+ -2.40E-08], Orthogonalization Method: 0}
+ - { #--------------------------------------------------------------------- iter: 10
+ GPU acceleration: No, Total electronic charge: 10.000207829537,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45594819534E+01, Epot: -2.16405200901E+01, Enl: 1.75360305267E+00,
+ EH: 1.72813947130E+01, EXC: -4.77531316822E+00, EvXC: -6.25519991206E+00},
+ iter: 10, EKS: -1.98842956423030017E+01, gnrm: 2.95E-04, D: -1.33E-06,
+ DIIS weights: [ 1.13E-02, 2.97E-02, -1.01E-02, -3.40E-01, 1.30E-01, 1.18E+00,
+ -3.18E-09], Orthogonalization Method: 0}
+ - { #--------------------------------------------------------------------- iter: 11
+ GPU acceleration: No, Total electronic charge: 10.000207999580,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45595032084E+01, Epot: -2.16404949307E+01, Enl: 1.75345166378E+00,
+ EH: 1.72812892357E+01, EXC: -4.77531087125E+00, EvXC: -6.25519693769E+00},
+ iter: 11, EKS: -1.98842958169594937E+01, gnrm: 9.17E-05, D: -1.75E-07,
+ DIIS weights: [ 7.75E-03, 2.46E-02, -3.45E-02, -1.09E-01, 1.42E-01, 9.69E-01,
+ -4.47E-10], Orthogonalization Method: 0}
+ - &FINAL001 { #---------------------------------------------------------- iter: 12
+ GPU acceleration: No, Total electronic charge: 10.000207942996,
+ Poisson Solver: {BC: Periodic, Box: [ 60, 60, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes,
+ iter: 12, EKS: -1.98842958295531673E+01, gnrm: 9.17E-05, D: -1.26E-08, #FINAL
+ Energies: {Ekin: 1.45594714734E+01, Epot: -2.16404640612E+01, Enl: 1.75341675641E+00,
+ EH: 1.72812518007E+01, EXC: -4.77530559676E+00, EvXC: -6.25518998850E+00,
+ Eion: 1.24464741081E+00},
+ }
+ Non-Hermiticity of Hamiltonian in the Subspace: 2.36E-31
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.010350904622E+00, f: 2.0000}, # 00001
+ {e: -4.753468810105E-01, f: 2.0000}, # 00002
+ {e: -4.091925033294E-01, f: 2.0000}, # 00003
+ {e: -4.091920882458E-01, f: 2.0000}, # 00004
+ {e: -3.597055384823E-01, f: 2.0000}] # 00005
+ Last Iteration : *FINAL001
+ #---------------------------------------------------------------------- Forces Calculation
+ GPU acceleration : No
+ Total electronic charge : 10.000207942996
+ Poisson Solver:
+ BC : Periodic
+ Box : [ 60, 60, 60 ]
+ MPI tasks : 1
+ Multipole analysis origin : [ 0.0E+00, 0.000000E+00, 1.053513E+00 ]
+ Electric Dipole Moment (AU):
+ P vector : [ -5.8862E+01, -5.8862E+01, -3.1150E+01 ]
+ norm(P) : 8.888135E+01
+ Electric Dipole Moment (Debye):
+ P vector : [ -1.4961E+02, -1.4961E+02, -7.9175E+01 ]
+ norm(P) : 2.259138E+02
+ Quadrupole Moment (AU):
+ Q matrix:
+ - [-3.9219E+02, -1.0388E+03, -5.4943E+02]
+ - [-1.0388E+03, -3.9219E+02, -5.4943E+02]
+ - [-5.4943E+02, -5.4943E+02, 7.8437E+02]
+ trace : -3.65E-11
+ Calculate local forces : Yes
+ Calculate Non Local forces : Yes
+ Stress Tensor calculated : Yes
+ Stress Tensor:
+ Total stress tensor matrix (Ha/Bohr^3):
+ - [ 3.163880073277E-06, 0.00000000000, -7.888610933001E-31 ]
+ - [ 0.00000000000, 3.163880073278E-06, 0.00000000000 ]
+ - [ -7.888610933001E-31, 0.00000000000, 5.613640065878E-05 ]
+ Pressure:
+ Ha/Bohr^3 : 2.08213869351100E-05
+ GPa : 0.612586
+ PV (Ha) : 4.81948214974662E-02
+ #-------------------------------- Warnings obtained during the run, check their relevance!
+ WARNINGS:
+ - The coarse grid does not fill the entire periodic box
+ #-------------------------------------------------------------------- Timing for root process
+ Timings for root process:
+ CPU time (s) : 29.32
+ Elapsed time (s) : 4.11
+ BigDFT infocode : 0
+ Average noise forces: {x: 2.65895237E-04, y: 2.65895237E-04, z: 7.51945326E-04,
+ total: 8.40727261E-04}
+ Clean forces norm (Ha/Bohr): {maxval: 5.679354138515E-02, fnrm2: 6.331351257208E-03}
+ #------------------------------------------------------------------------------ Atomic Forces
+ Atomic Forces (Ha/Bohr):
+ - {N: [ 0.000000000000E+00, 0.000000000000E+00, 5.626119625775E-02]} # 0001
+ - {N: [ 0.000000000000E+00, 0.000000000000E+00, -5.626119625775E-02]} # 0002
+ Energy (Hartree) : -1.98842958295531673E+01
+ Force Norm (Hartree/Bohr) : 7.95653467830459704E-02
+ Memory Consumption Report:
+ Tot. No. of Allocations : 1590
+ Tot. No. of Deallocations : 1590
+ Remaining Memory (B) : 0
+ Memory occupation:
+ Peak Value (MB) : 70.631
+ for the array : wz
+ in the routine : input_wf
+ Memory Peak of process : 66.424 MB
+ Walltime since initialization : 00:00:04.794040984
+ Max No. of dictionaries used : 4502 #( 1019 still in use)
+ Number of dictionary folders allocated: 1
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..cb14692847f065ec3627336201f6dc7cea7c0427
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/posinp.xyz
@@ -0,0 +1,4 @@
+2 angstroem
+periodic 7 7 7
+N 0. 0. 0.
+N 0. 0. 1.11499
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..cb780395b7c1f8bc5cb4417719077afd4d84630d
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/periodic/time.yaml
@@ -0,0 +1,433 @@
+---
+ INIT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 7.2, 3.69E-02]
+ Communications : [ 0.0, 3.81E-06]
+ BLAS-LAPACK : [ 0.9, 4.81E-03]
+ PS Computation : [ 1.3, 6.82E-03]
+ Potential : [ 2.4, 1.20E-02]
+ Convolutions : [ 22.3, 0.11]
+ Other : [ 16.7, 8.53E-02]
+ Initialization : [ 12.5, 6.41E-02]
+ Total : [ 63.4, 0.51]
+ Categories: #Ordered by time consumption
+ ionic_energy:
+ Data : [ 16.5, 8.45E-02]
+ Class : Other
+ Info : Miscellaneous
+ ApplyLocPotKin:
+ Data : [ 13.0, 6.64E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ wavefunction:
+ Data : [ 11.9, 6.10E-02]
+ Class : Initialization
+ Info : Miscellaneous
+ Rho_comput:
+ Data : [ 9.3, 4.76E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Init to Zero:
+ Data : [ 5.1, 2.61E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Exchange-Correlation:
+ Data : [ 2.4, 1.20E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ Array allocations:
+ Data : [ 1.1, 5.86E-03]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ PSolver Computation:
+ Data : [ 1.1, 5.78E-03]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.9, 4.81E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Routine Profiling:
+ Data : [ 0.7, 3.49E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Vector copy:
+ Data : [ 0.3, 1.47E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Input_comput:
+ Data : [ 0.3, 1.37E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ CrtLocPot:
+ Data : [ 0.3, 1.32E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ PSolver Kernel Creation:
+ Data : [ 0.2, 1.04E-03]
+ Class : PS Computation
+ Info : ISF operations and creation of the kernel
+ ApplyProj:
+ Data : [ 0.1, 7.33E-04]
+ Class : Other
+ Info : RMA pattern
+ CrtDescriptors:
+ Data : [ 0.1, 3.82E-04]
+ Class : Initialization
+ Info : RMA Pattern
+ calc_bounds:
+ Data : [ 0.0, 3.55E-05]
+ Class : Other
+ Info : Miscellaneous
+ Un-TransSwitch:
+ Data : [ 0.0, 2.43E-05]
+ Class : Other
+ Info : RMA pattern
+ Pot_after_comm:
+ Data : [ 0.0, 7.15E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 3.81E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ WFN_OPT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 7.8, 0.26]
+ Communications : [ 0.0, 5.58E-05]
+ BLAS-LAPACK : [ 0.3, 9.67E-03]
+ PS Computation : [ 1.1, 3.53E-02]
+ Potential : [ 4.0, 0.13]
+ Convolutions : [ 78.5, 2.6]
+ Linear Algebra : [ 0.3, 9.88E-03]
+ Other : [ 7.4, 0.24]
+ Total : [ 99.3, 3.3]
+ Categories: #Ordered by time consumption
+ Precondition:
+ Data : [ 50.5, 1.7]
+ Class : Convolutions
+ Info : OpenCL ported
+ Rho_comput:
+ Data : [ 14.0, 0.46]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyLocPotKin:
+ Data : [ 14.0, 0.46]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyProj:
+ Data : [ 6.6, 0.22]
+ Class : Other
+ Info : RMA pattern
+ Init to Zero:
+ Data : [ 5.2, 0.17]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Exchange-Correlation:
+ Data : [ 4.0, 0.13]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ Routine Profiling:
+ Data : [ 1.1, 3.59E-02]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ PSolver Computation:
+ Data : [ 1.1, 3.53E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Array allocations:
+ Data : [ 0.9, 3.12E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Diis:
+ Data : [ 0.7, 2.45E-02]
+ Class : Other
+ Info : Other
+ Vector copy:
+ Data : [ 0.6, 1.83E-02]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Chol_comput:
+ Data : [ 0.3, 9.77E-03]
+ Class : Linear Algebra
+ Info : ALLReduce orbs
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.3, 9.67E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Un-TransSwitch:
+ Data : [ 0.0, 2.79E-04]
+ Class : Other
+ Info : RMA pattern
+ LagrM_comput:
+ Data : [ 0.0, 1.13E-04]
+ Class : Linear Algebra
+ Info : DGEMM
+ Pot_after_comm:
+ Data : [ 0.0, 8.49E-05]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.58E-05]
+ Class : Communications
+ Info : AllGathrv grid
+ LAST: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 12.6, 3.56E-02]
+ Communications : [ 0.0, 3.62E-05]
+ BLAS-LAPACK : [ 0.3, 9.77E-04]
+ PS Computation : [ 1.7, 4.70E-03]
+ Potential : [ 4.2, 1.20E-02]
+ Convolutions : [ 47.1, 0.13]
+ Other : [ 7.3, 2.07E-02]
+ Finalization : [ 21.4, 6.04E-02]
+ Total : [ 94.7, 0.28]
+ Categories: #Ordered by time consumption
+ Rho_comput:
+ Data : [ 29.9, 8.44E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Forces:
+ Data : [ 21.4, 6.04E-02]
+ Class : Finalization
+ Info : Miscellaneous
+ ApplyLocPotKin:
+ Data : [ 17.2, 4.87E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Init to Zero:
+ Data : [ 9.8, 2.76E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ ApplyProj:
+ Data : [ 7.3, 2.07E-02]
+ Class : Other
+ Info : RMA pattern
+ Exchange-Correlation:
+ Data : [ 4.2, 1.20E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ PSolver Computation:
+ Data : [ 1.7, 4.70E-03]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Routine Profiling:
+ Data : [ 1.2, 3.47E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Array allocations:
+ Data : [ 1.2, 3.39E-03]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Vector copy:
+ Data : [ 0.4, 1.13E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.3, 9.49E-04]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Lapack (dsy-ssy-che-zhe)eev:
+ Data : [ 0.0, 2.77E-05]
+ Class : BLAS-LAPACK
+ Info : Lapack Eigenvalue Problem
+ Allreduce, Small Size:
+ Data : [ 0.0, 2.53E-05]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ Un-TransSwitch:
+ Data : [ 0.0, 1.24E-05]
+ Class : Other
+ Info : RMA pattern
+ Pot_after_comm:
+ Data : [ 0.0, 8.11E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 7.39E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Large Size:
+ Data : [ 0.0, 3.58E-06]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ SUMMARY: # % , Time (s)
+ INIT : [ 12.5, 0.51]
+ WFN_OPT : [ 80.7, 3.3]
+ LAST : [ 6.9, 0.28]
+ Total : [ 100.0, 4.1]
+ Routines timing and number of calls:
+ - Main_program: [ 4.78, 1, ~*]
+ Subroutines:
+ - process_run (id="posinp"): [ 4.11, 1, 86.04%*]
+ Subroutines:
+ - bigdft_state: [ 4.11, 1, 100.07%*]
+ Subroutines:
+ - quantum_mechanical_state: [ 4.10, 1, 99.82%*]
+ Subroutines:
+ - cluster: [ 4.10, 1, 100.03%]
+ Subroutines:
+ - preconditionall2: [ 1.73, 11, 42.10%]
+ Subroutines:
+ - precondition_preconditioner: [ 4.489E-02, 55, 2.59%]
+ - calculate_rmr_new: [ 2.512E-02, 330, 1.45%]
+ - finalise_precond_residue: [ 2.116E-03, 55, 0.12%]
+ - LocalHamiltonianApplication: [ 0.574, 12, 13.99%]
+ Subroutines:
+ - psir_to_vpsi: [ 1.739E-02, 60, 3.03%]
+ Subroutines:
+ - apply_potential_lr_nobounds: [ 1.353E-02, 60, 77.79%]
+ - orbital_basis_associate: [ 7.744E-04, 12, 0.13%]
+ - input_wf: [ 0.386, 1, 9.41%]
+ Subroutines:
+ - LocalHamiltonianApplication: [ 6.752E-02, 1, 17.49%]
+ Subroutines:
+ - psir_to_vpsi: [ 2.117E-03, 8, 3.14%]
+ Subroutines:
+ - apply_potential_lr_nobounds: [ 1.663E-03, 8, 78.55%]
+ - orbital_basis_associate: [ 6.650E-05, 1, 0.10%]
+ - updatePotential: [ 2.708E-02, 1, 7.01%]
+ Subroutines:
+ - XC_potential: [ 2.291E-02, 1, 84.60%]
+ Subroutines:
+ - xc_energy_new: [ 1.195E-02, 1, 52.17%]
+ Subroutines:
+ - xc_getvxc: [ 1.136E-02, 1, 95.03%]
+ - Electrostatic_Solver: [ 3.441E-03, 1, 12.71%]
+ Subroutines:
+ - apply_kernel: [ 2.848E-03, 1, 82.76%]
+ Subroutines:
+ - G_PoissonSolver: [ 2.502E-03, 1, 87.85%]
+ - daub_to_isf: [ 2.114E-02, 8, 5.48%]
+ - LDiagHam: [ 6.484E-03, 1, 1.68%]
+ - NonLocalHamiltonianApplication: [ 1.044E-03, 1, 0.27%]
+ Subroutines:
+ - atom_projector: [ 3.887E-04, 2, 37.24%]
+ Subroutines:
+ - crtproj: [ 2.986E-04, 2, 76.83%]
+ - orbital_basis_associate: [ 7.377E-05, 1, 7.07%]
+ - local_potential_dimensions: [ 1.575E-04, 3, 0.04%]
+ - check_linear_and_create_Lzd: [ 1.339E-04, 1, 0.03%]
+ - deallocate_work_arrays_sumrho: [ 9.117E-05, 1, 0.02%]
+ - initialize_work_arrays_sumrho: [ 6.331E-05, 1, 0.02%]
+ - full_local_potential: [ 5.034E-05, 1, 0.01%]
+ - SynchronizeHamiltonianApplication: [ 1.654E-05, 1, 0.00%]
+ - NonLocalHamiltonianApplication: [ 0.261, 12, 6.37%]
+ Subroutines:
+ - atom_projector: [ 0.216, 24, 82.94%]
+ Subroutines:
+ - crtproj: [ 0.213, 24, 98.54%]
+ - orbital_basis_associate: [ 8.420E-04, 12, 0.32%]
+ - XC_potential: [ 0.246, 12, 6.00%]
+ Subroutines:
+ - xc_energy_new: [ 0.145, 12, 58.78%]
+ Subroutines:
+ - xc_getvxc: [ 0.136, 12, 93.99%]
+ - daub_to_isf: [ 0.170, 60, 4.14%]
+ - kswfn_post_treatments: [ 0.121, 1, 2.95%]
+ Subroutines:
+ - calculate_forces: [ 6.260E-02, 1, 51.73%]
+ Subroutines:
+ - local_hamiltonian_stress: [ 4.059E-02, 1, 64.84%]
+ - erf_stress: [ 1.521E-02, 1, 24.30%]
+ - nonlocal_forces: [ 4.508E-03, 1, 7.20%]
+ Subroutines:
+ - atom_projector: [ 3.232E-03, 20, 71.70%]
+ Subroutines:
+ - crtproj: [ 2.563E-03, 20, 79.29%]
+ - local_forces: [ 1.915E-03, 1, 3.06%]
+ - rhocore_forces: [ 1.855E-05, 1, 0.03%]
+ - daub_to_isf: [ 1.470E-02, 5, 12.15%]
+ - calculate_dipole_moment: [ 1.091E-02, 1, 9.01%]
+ - Electrostatic_Solver: [ 3.142E-03, 1, 2.60%]
+ Subroutines:
+ - apply_kernel: [ 2.808E-03, 1, 89.35%]
+ Subroutines:
+ - G_PoissonSolver: [ 2.464E-03, 1, 87.76%]
+ - deallocate_work_arrays_sumrho: [ 9.477E-05, 1, 0.08%]
+ - orbital_basis_associate: [ 8.475E-05, 1, 0.07%]
+ - initialize_work_arrays_sumrho: [ 5.324E-05, 1, 0.04%]
+ - IonicEnergyandForces: [ 8.467E-02, 1, 2.07%]
+ Subroutines:
+ - vdwcorrection_calculate_energy: [ 2.615E-05, 1, 0.03%]
+ - vdwcorrection_calculate_forces: [ 1.448E-05, 1, 0.02%]
+ - Electrostatic_Solver: [ 6.784E-02, 12, 1.65%]
+ Subroutines:
+ - apply_kernel: [ 5.950E-02, 12, 87.71%]
+ Subroutines:
+ - G_PoissonSolver: [ 3.865E-02, 12, 64.96%]
+ - system_initialization: [ 3.293E-02, 1, 0.80%]
+ Subroutines:
+ - createProjectorsArrays: [ 1.509E-03, 1, 4.58%]
+ Subroutines:
+ - localize_projectors: [ 3.376E-04, 1, 22.37%]
+ Subroutines:
+ - fill_logrid: [ 1.209E-04, 4, 35.81%]
+ - num_segkeys: [ 1.025E-04, 4, 30.36%]
+ - segkeys: [ 1.785E-04, 4, 11.83%]
+ - set_wfd_to_wfd: [ 1.728E-04, 2, 11.45%]
+ Subroutines:
+ - init_tolr: [ 1.000E-04, 2, 57.87%]
+ - fill_logrid: [ 1.200E-04, 4, 7.95%]
+ - transform_keyglob_to_keygloc: [ 9.776E-05, 4, 6.48%]
+ - allocate_arrays: [ 7.743E-05, 1, 5.13%]
+ - gaussian_basis_from_psp: [ 3.939E-05, 1, 2.61%]
+ - nullify_structure: [ 1.636E-05, 1, 1.08%]
+ - pkernel_set: [ 1.231E-03, 1, 3.74%]
+ Subroutines:
+ - mpi_environment_set: [ 1.579E-05, 1, 1.28%]
+ - createWavefunctionsDescriptors: [ 7.456E-04, 1, 2.26%]
+ Subroutines:
+ - fill_logrid: [ 1.740E-04, 2, 23.34%]
+ - num_segkeys: [ 1.648E-04, 2, 22.10%]
+ - segkeys: [ 1.124E-04, 2, 15.08%]
+ - orbital_basis_associate: [ 6.065E-05, 1, 0.18%]
+ - mpi_environment_set: [ 1.792E-05, 1, 0.05%]
+ - createEffectiveIonicPotential: [ 7.122E-03, 1, 0.17%]
+ Subroutines:
+ - createIonicPotential: [ 7.085E-03, 1, 99.48%]
+ Subroutines:
+ - Electrostatic_Solver: [ 5.467E-03, 1, 77.17%]
+ Subroutines:
+ - apply_kernel: [ 5.108E-03, 1, 93.43%]
+ Subroutines:
+ - G_PoissonSolver: [ 3.223E-03, 1, 63.10%]
+ - timing_dump_results: [ 1.606E-03, 2, 0.04%]
+ - deallocate_work_arrays_sumrho: [ 1.186E-03, 12, 0.03%]
+ - full_local_potential: [ 8.804E-04, 12, 0.02%]
+ - initialize_work_arrays_sumrho: [ 7.674E-04, 12, 0.02%]
+ - SynchronizeHamiltonianApplication: [ 2.895E-04, 12, 0.01%]
+ - interaction_multipoles_ions: [ 6.620E-05, 1, 0.00%]
+ - ionic_energy_of_external_charges: [ 3.607E-05, 1, 0.00%]
+ - potential_from_charge_multipoles: [ 1.689E-05, 1, 0.00%]
+ - timing_dump_results: [ 7.609E-04, 1, 0.02%]
+ - bigdft_init: [ 0.612, 1, 12.80%]
+ Subroutines:
+ - mpi_environment_set: [ 2.486E-05, 1, 0.00%]
+ - run_objects_init: [ 5.764E-02, 1, 1.21%]
+ Subroutines:
+ - set_run_objects: [ 3.128E-02, 1, 54.26%]
+ Subroutines:
+ - inputs_from_dict: [ 3.122E-02, 1, 99.81%]
+ Subroutines:
+ - input_keys_dump: [ 1.474E-02, 1, 47.21%]
+ - input_keys_fill_all: [ 9.713E-03, 1, 31.11%]
+ Subroutines:
+ - input_keys_init: [ 5.265E-03, 1, 54.20%]
+ - PS_input_dict: [ 9.306E-04, 1, 9.58%]
+ - astruct_set_from_dict: [ 1.892E-03, 1, 6.06%]
+ - psp_dict_fill_all: [ 2.323E-04, 1, 0.74%]
+ - psp_dict_analyse: [ 2.268E-04, 1, 0.73%]
+ - allocateBasicArraysInputLin: [ 8.176E-05, 1, 0.26%]
+ - atomic_data_set_from_dict: [ 6.385E-05, 1, 0.20%]
+ - kpt_input_analyse: [ 5.519E-05, 1, 0.18%]
+ - occupation_set_from_dict: [ 3.294E-05, 1, 0.11%]
+ - atomic_gamma_from_dict: [ 2.575E-05, 1, 0.08%]
+ - input_analyze: [ 1.880E-05, 1, 0.06%]
+ - read_n_orbitals: [ 1.579E-05, 1, 0.05%]
+ - astruct_file_merge_to_dict: [ 2.580E-02, 1, 44.77%]
+ - read_input_dict_from_files: [ 5.130E-05, 1, 0.09%]
+ CPU parallelism:
+ MPI tasks : 1
+ OMP threads : 8
+ Report timestamp : 2016-12-02 09:05:22.883
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/forces_posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/forces_posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..f198f9c885247decbab2ffec2a28df76fc260119
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/forces_posinp.xyz
@@ -0,0 +1,7 @@
+ 2 angstroemd0 -1.98841356435336820E+01 (Ha) Geometry + metaData forces
+surface 7.00000000000000000E+00 7.14389234742000045E+00 7.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
+ forces
+N 0.00000000000000000E+00 -1.05879118406787542E-22 5.62509981015626437E-02
+N 0.00000000000000000E+00 2.11758236813575085E-22 -5.62509981015626437E-02
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/input_minimal.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/input_minimal.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..224705f2bb20dba207c02b9130629fa6c7e0b119
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/input_minimal.yaml
@@ -0,0 +1,17 @@
+ #---------------------------------------------------------------------- Minimal input file
+ #This file indicates the minimal set of input variables which has to be given to perform
+ #the run. The code would produce the same output if this file is used as input.
+ posinp:
+ units: angstroem
+ cell: [ 7.0, .inf, 7.0]
+ positions:
+ - N: [0.0, 0.0, 0.0]
+ - N: [0.0, 0.0, 1.114989995956421]
+ properties:
+ format: xyz
+ source: posinp.xyz
+ psolver:
+ environment:
+ gammaS: water
+ alphaS: water
+ betaV: water
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/output.out b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..523acab961a276f22c930031ad96a4e51324e884
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/output.out
@@ -0,0 +1,720 @@
+---
+ 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 : 2016-12-02 09:06:15.085
+ 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
+ cell: [ 7.0, .inf, 7.0]
+ 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 : Surface #Code: S
+ Box Sizes (AU) : [ 1.32281E+01, 0.00000E+00, 1.32281E+01 ]
+ Number of Symmetries : 8
+ Space group : P m m m
+ #------------------------------ 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
+ #------------------- K points description (Reduced and Brillouin zone coordinates, Weight)
+ K points:
+ - {Rc: [ 0.0000, 0.0000, 0.0000 ], Bz: [ 0.0000, 0.0000, 0.0000 ], Wgt: 1.0000} # 0001
+ 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
+ #----------------------------------------------------------------------- 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
+ Cell: [ 7.0, .inf, 7.0]
+ Positions:
+ - N: [ 0.000000000, 3.571946174, 0.000000000] # [ 0.00, 15.00, 0.00 ] 0001
+ - N: [ 0.000000000, 3.571946174, 1.114989996] # [ 0.00, 15.00, 4.78 ] 0002
+ Rigid Shift Applied (AU) : [ -0.0000, 6.7500, -0.0000 ]
+ #------------------------------------------------------------------------- Grid properties
+ Box Grid spacings : [ 0.4409, 0.4500, 0.4409 ]
+ Sizes of the simulation domain:
+ AU : [ 13.228, 13.500, 13.228 ]
+ Angstroem : [ 7.0000, 7.1439, 7.0000 ]
+ Grid Spacing Units : [ 29, 30, 29 ]
+ High resolution region boundaries (GU):
+ From : [ 0, 11, 0 ]
+ To : [ 29, 19, 29 ]
+ High Res. box is treated separately : No
+ #------------------------------------------------------------------- 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 : Surface
+ Memory Requirements per MPI task:
+ Density (MB) : 2.64
+ Kernel (MB) : 0.71
+ Full Grid Arrays (MB) : 2.50
+ Wavefunctions Descriptors, full simulation domain:
+ Coarse resolution grid:
+ No. of segments : 1563
+ No. of points : 18111
+ Fine resolution grid:
+ No. of segments : 222
+ No. of points : 738
+ #---------------------------------------------------------------------- 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:
+ #Kpt #0001 BZ coord. = [ 0.000000, 0.000000, 0.000000 ]
+ - Occupation Numbers: {Orbitals No. 1-5: 2.0000}
+ Wavefunctions memory occupation for root MPI process: 0 MB 909 KB 264 B
+ NonLocal PSP Projectors Descriptors:
+ Creation strategy : On-the-fly
+ Total number of projectors : 2
+ Total number of components : 6226
+ Percent of zero components : 14
+ Size of workspaces : 24920
+ Maximum size of masking arrays for a projector: 1950
+ Cumulative size of masking arrays : 3876
+ 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 : 0.182 # (Number of Components: 23277)
+ All (distributed) orbitals : 1.795 # (Number of Orbitals per MPI task: 5)
+ Wavefunction storage size : 12.442 # (DIIS/SD workspaces included)
+ Nonlocal Pseudopotential Arrays : 0.49
+ Full Uncompressed (ISF) grid : 2.512
+ Workspaces storage size : 0.640
+ Accumulated memory requirements during principal run stages (MiB.KiB):
+ Kernel calculation : 7.843
+ Density Construction : 26.102
+ Poisson Solver : 34.291
+ Hamiltonian application : 28.613
+ Orbitals Orthonormalization : 28.613
+ Estimated Memory Peak (MB) : 34
+ Poisson Solver:
+ BC : Surface
+ Box : [ 60, 91, 60 ]
+ MPI tasks : 1
+ Ion-Ion interaction energy : -2.76590584390539E+00
+ #---------------------------------------------------------------- Ionic Potential Creation
+ Total ionic charge : -10.000000000000
+ Poisson Solver:
+ BC : Surface
+ Box : [ 60, 91, 60 ]
+ 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 : 8.65E-05
+ GPU acceleration : No
+ Total electronic charge : 10.000108742710
+ Poisson Solver:
+ BC : Surface
+ Box : [ 60, 91, 60 ]
+ MPI tasks : 1
+ Energies: {Ekin: 1.39080908189E+01, Epot: -2.18666636568E+01, Enl: 2.33303618823E+00,
+ EH: 1.26725700969E+01, EXC: -4.69916957910E+00, EvXC: -6.15455937830E+00}
+ EKS : -1.96086227912682141E+01
+ Input Guess Overlap Matrices: {Calculated: Yes, Diagonalized: Yes}
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.040699695870E+00, f: 2.0000}, # 00001
+ {e: -5.271901792360E-01, f: 2.0000}, # 00002
+ {e: -4.411280461794E-01, f: 2.0000}, # 00003
+ {e: -4.410546016559E-01, f: 2.0000}, # 00004
+ {e: -3.947626380105E-01, f: 2.0000}, # 00005
+ {e: -1.012179545565E-01, f: 0.0000}, # 00006
+ {e: -1.011175286645E-01, f: 0.0000}, # 00007
+ {e: 6.784834237651E-01, f: 0.0000}] # 00008
+ IG wavefunctions defined : Yes
+ #------------------------------------------------------------------- Self-Consistent Cycle
+ Ground State Optimization:
+ - Hamiltonian Optimization: &itrp001
+ - Subspace Optimization: &itrep001-01
+ Wavefunctions Iterations:
+ - { #---------------------------------------------------------------------- iter: 1
+ GPU acceleration: No, Total electronic charge: 10.000389933695,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.31538492588E+01, Epot: -2.15573055961E+01, Enl: 1.86122392960E+00,
+ EH: 1.17200077630E+01, EXC: -4.58244716816E+00, EvXC: -6.00045308465E+00},
+ iter: 1, EKS: -1.96101400981659637E+01, gnrm: 3.17E-01, D: -1.52E-03,
+ DIIS weights: [ 1.00E+00, 1.00E+00], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 2
+ GPU acceleration: No, Total electronic charge: 10.000296346079,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.49527037296E+01, Epot: -2.17338581195E+01, Enl: 1.91067969412E+00,
+ EH: 1.37238873719E+01, EXC: -4.89104810686E+00, EvXC: -6.40779434885E+00},
+ iter: 2, EKS: -1.98435216696016212E+01, gnrm: 1.02E-01, D: -2.33E-01,
+ DIIS weights: [ 3.49E-01, 6.51E-01, -1.45E-02], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 3
+ GPU acceleration: No, Total electronic charge: 10.000203070155,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.43167701030E+01, Epot: -2.17350710769E+01, Enl: 1.76296046012E+00,
+ EH: 1.29313304918E+01, EXC: -4.75185124119E+00, EvXC: -6.22424933354E+00},
+ iter: 3, EKS: -1.98801787570613442E+01, gnrm: 5.03E-02, D: -3.67E-02,
+ DIIS weights: [ 6.68E-02, 1.69E-01, 7.64E-01, -9.50E-04], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 4
+ GPU acceleration: No, Total electronic charge: 10.000219687126,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45120839965E+01, Epot: -2.17882568714E+01, Enl: 1.77013639922E+00,
+ EH: 1.30929666594E+01, EXC: -4.78073509220E+00, EvXC: -6.26232752805E+00},
+ iter: 4, EKS: -1.98833165431556935E+01, gnrm: 2.59E-02, D: -3.14E-03,
+ DIIS weights: [-1.29E-02, -3.33E-02, 1.69E-01, 8.77E-01, -8.56E-05],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 5
+ GPU acceleration: No, Total electronic charge: 10.000204535242,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45244128407E+01, Epot: -2.18218754496E+01, Enl: 1.75935924554E+00,
+ EH: 1.30596171638E+01, EXC: -4.77450069450E+00, EvXC: -6.25412530503E+00},
+ iter: 5, EKS: -1.98840017605869548E+01, gnrm: 1.08E-02, D: -6.85E-04,
+ DIIS weights: [-7.23E-03, -1.85E-02, -5.19E-02, 1.43E-01, 9.34E-01, -7.59E-06],
+ Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 6
+ GPU acceleration: No, Total electronic charge: 10.000203581433,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45444096446E+01, Epot: -2.18366276779E+01, Enl: 1.75613302365E+00,
+ EH: 1.30618483502E+01, EXC: -4.77482832955E+00, EvXC: -6.25455952376E+00},
+ iter: 6, EKS: -1.98841080095792826E+01, gnrm: 4.09E-03, D: -1.06E-04,
+ DIIS weights: [ 1.12E-03, 6.90E-03, -1.67E-02, -8.50E-02, 6.78E-02, 1.03E+00,
+ -8.47E-07], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 7
+ GPU acceleration: No, Total electronic charge: 10.000204807633,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45528807898E+01, Epot: -2.18423658495E+01, Enl: 1.75515037186E+00,
+ EH: 1.30637276373E+01, EXC: -4.77517405458E+00, EvXC: -6.25501566644E+00},
+ iter: 7, EKS: -1.98841265572481802E+01, gnrm: 1.78E-03, D: -1.85E-05,
+ DIIS weights: [ 1.27E-04, 9.72E-05, -1.00E-02, -6.45E-02, 1.46E-02, 1.06E+00,
+ -2.70E-07], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 8
+ GPU acceleration: No, Total electronic charge: 10.000205947400,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45560723299E+01, Epot: -2.18449492182E+01, Enl: 1.75458753021E+00,
+ EH: 1.30637971341E+01, EXC: -4.77523209379E+00, EvXC: -6.25509274164E+00},
+ iter: 8, EKS: -1.98841316882522534E+01, gnrm: 1.08E-03, D: -5.13E-06,
+ DIIS weights: [ 3.69E-03, 7.04E-03, -3.06E-02, -1.57E-01, -6.72E-02, 1.24E+00,
+ -9.00E-08], Orthogonalization Method: 0}
+ - { #---------------------------------------------------------------------- iter: 9
+ GPU acceleration: No, Total electronic charge: 10.000206932270,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45573957032E+01, Epot: -2.18460650928E+01, Enl: 1.75402783503E+00,
+ EH: 1.30634392675E+01, EXC: -4.77520580877E+00, EvXC: -6.25505817444E+00},
+ iter: 9, EKS: -1.98841343002990669E+01, gnrm: 6.64E-04, D: -2.61E-06,
+ DIIS weights: [ 4.27E-03, 2.50E-02, -2.82E-02, -3.65E-01, -1.08E-01, 1.47E+00,
+ -2.20E-08], Orthogonalization Method: 0}
+ - { #--------------------------------------------------------------------- iter: 10
+ GPU acceleration: No, Total electronic charge: 10.000207735505,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45584612998E+01, Epot: -2.18466334589E+01, Enl: 1.75365204537E+00,
+ EH: 1.30635811809E+01, EXC: -4.77526584027E+00, EvXC: -6.25513749809E+00},
+ iter: 10, EKS: -1.98841354807016906E+01, gnrm: 2.78E-04, D: -1.18E-06,
+ DIIS weights: [ 1.07E-02, 2.93E-02, -9.67E-03, -3.37E-01, 1.49E-01, 1.16E+00,
+ -2.84E-09], Orthogonalization Method: 0}
+ - { #--------------------------------------------------------------------- iter: 11
+ GPU acceleration: No, Total electronic charge: 10.000207872980,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes, Orthoconstraint: Yes, Preconditioning: Yes,
+ Energies: {Ekin: 1.45584485081E+01, Epot: -2.18465942609E+01, Enl: 1.75350630878E+00,
+ EH: 1.30634599902E+01, EXC: -4.77525938002E+00, EvXC: -6.25512902567E+00},
+ iter: 11, EKS: -1.98841356325770136E+01, gnrm: 8.58E-05, D: -1.52E-07,
+ DIIS weights: [ 7.95E-03, 2.28E-02, -4.37E-02, -8.76E-02, 1.38E-01, 9.62E-01,
+ -3.97E-10], Orthogonalization Method: 0}
+ - &FINAL001 { #---------------------------------------------------------- iter: 12
+ GPU acceleration: No, Total electronic charge: 10.000207819173,
+ Poisson Solver: {BC: Surface, Box: [ 60, 91, 60 ], MPI tasks: 1},
+ Hamiltonian Applied: Yes,
+ iter: 12, EKS: -1.98841356435336820E+01, gnrm: 8.58E-05, D: -1.10E-08, #FINAL
+ Energies: {Ekin: 1.45584230973E+01, Epot: -2.18465683644E+01, Enl: 1.75347571901E+00,
+ EH: 1.30634285224E+01, EXC: -4.77525504423E+00, EvXC: -6.25512331509E+00,
+ Eion: -2.76590584391E+00},
+ }
+ Non-Hermiticity of Hamiltonian in the Subspace: 3.44E-31
+ #Eigenvalues and New Occupation Numbers
+ Orbitals: [
+ {e: -1.031076340591E+00, f: 2.0000}, # 00001
+ {e: -4.960695733103E-01, f: 2.0000}, # 00002
+ {e: -4.299111610704E-01, f: 2.0000}, # 00003
+ {e: -4.298492754446E-01, f: 2.0000}, # 00004
+ {e: -3.804284236223E-01, f: 2.0000}] # 00005
+ Last Iteration : *FINAL001
+ #---------------------------------------------------------------------- Forces Calculation
+ GPU acceleration : No
+ Total electronic charge : 10.000207819173
+ Poisson Solver:
+ BC : Surface
+ Box : [ 60, 91, 60 ]
+ MPI tasks : 1
+ Multipole analysis origin : [ 0.0E+00, 6.750000E+00, 1.053513E+00 ]
+ Electric Dipole Moment (AU):
+ P vector : [ -5.8863E+01, -5.1869E-04, -3.1151E+01 ]
+ norm(P) : 6.659702E+01
+ Electric Dipole Moment (Debye):
+ P vector : [ -1.4961E+02, -1.3184E-03, -7.9177E+01 ]
+ norm(P) : 1.692727E+02
+ Quadrupole Moment (AU):
+ Q matrix:
+ - [-1.0827E+03, -1.0093E-02, -5.4944E+02]
+ - [-1.0093E-02, 9.8886E+02, -7.0631E-03]
+ - [-5.4944E+02, -7.0631E-03, 9.3844E+01]
+ trace : -8.12E-11
+ Calculate local forces : Yes
+ Calculate Non Local forces : Yes
+ #-------------------------------------------------------------------- Timing for root process
+ Timings for root process:
+ CPU time (s) : 31.48
+ Elapsed time (s) : 4.64
+ BigDFT infocode : 0
+ Average noise forces: {x: 2.61935931E-04, y: 9.64089200E-06, z: 7.31920823E-04,
+ total: 7.77439046E-04}
+ Clean forces norm (Ha/Bohr): {maxval: 5.676885550852E-02, fnrm2: 6.328953924322E-03}
+ Raw forces norm (Ha/Bohr): {maxval: 5.676885625669E-02, fnrm2: 6.328954017269E-03}
+ #------------------------------------------------------------------------------ Atomic Forces
+ Atomic Forces (Ha/Bohr):
+ - {N: [ 0.000000000000E+00, -1.058791184068E-22, 5.625099810156E-02]} # 0001
+ - {N: [ 0.000000000000E+00, 2.117582368136E-22, -5.625099810156E-02]} # 0002
+ Energy (Hartree) : -1.98841356435336820E+01
+ Force Norm (Hartree/Bohr) : 7.95509244122531156E-02
+ Memory Consumption Report:
+ Tot. No. of Allocations : 4882
+ Tot. No. of Deallocations : 4882
+ Remaining Memory (B) : 0
+ Memory occupation:
+ Peak Value (MB) : 77.914
+ for the array : wz
+ in the routine : input_wf
+ Memory Peak of process : 78.172 MB
+ Walltime since initialization : 00:00:05.328530363
+ Max No. of dictionaries used : 4502 #( 1019 still in use)
+ Number of dictionary folders allocated: 1
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/posinp.xyz b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..22442838f292aa33965df6d233b7865e23258f13
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/posinp.xyz
@@ -0,0 +1,4 @@
+2 angstroem
+surface 7 7 7
+N 0. 0. 0.
+N 0. 0. 1.11499
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/time.yaml b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/time.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..a1f007faca229045a561d52492d427f506005ec5
--- /dev/null
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/surface/time.yaml
@@ -0,0 +1,438 @@
+---
+ INIT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 10.2, 6.80E-02]
+ Communications : [ 0.0, 4.05E-06]
+ BLAS-LAPACK : [ 0.7, 4.77E-03]
+ PS Computation : [ 17.7, 0.12]
+ Potential : [ 2.7, 1.82E-02]
+ Convolutions : [ 20.4, 0.14]
+ Other : [ 2.3, 1.57E-02]
+ Initialization : [ 13.9, 9.29E-02]
+ Total : [ 67.9, 0.67]
+ Categories: #Ordered by time consumption
+ PSolver Kernel Creation:
+ Data : [ 15.4, 0.10]
+ Class : PS Computation
+ Info : ISF operations and creation of the kernel
+ ApplyLocPotKin:
+ Data : [ 11.6, 7.78E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Rho_comput:
+ Data : [ 8.7, 5.84E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ wavefunction:
+ Data : [ 7.5, 5.01E-02]
+ Class : Initialization
+ Info : Miscellaneous
+ Array allocations:
+ Data : [ 6.9, 4.58E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ CrtDescriptors:
+ Data : [ 6.0, 4.01E-02]
+ Class : Initialization
+ Info : RMA Pattern
+ Exchange-Correlation:
+ Data : [ 2.7, 1.82E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ Init to Zero:
+ Data : [ 2.5, 1.66E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ PSolver Computation:
+ Data : [ 2.3, 1.57E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ ionic_energy:
+ Data : [ 2.2, 1.49E-02]
+ Class : Other
+ Info : Miscellaneous
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.7, 4.77E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Routine Profiling:
+ Data : [ 0.6, 3.94E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Vector copy:
+ Data : [ 0.2, 1.64E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ CrtLocPot:
+ Data : [ 0.2, 1.41E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ Input_comput:
+ Data : [ 0.2, 1.35E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ ApplyProj:
+ Data : [ 0.1, 6.69E-04]
+ Class : Other
+ Info : RMA pattern
+ Un-TransSwitch:
+ Data : [ 0.0, 4.41E-05]
+ Class : Other
+ Info : RMA pattern
+ calc_bounds:
+ Data : [ 0.0, 3.91E-05]
+ Class : Other
+ Info : Miscellaneous
+ Pot_after_comm:
+ Data : [ 0.0, 1.12E-05]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 4.05E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ WFN_OPT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 8.8, 0.33]
+ Communications : [ 0.0, 6.18E-05]
+ BLAS-LAPACK : [ 0.3, 9.68E-03]
+ PS Computation : [ 1.6, 6.09E-02]
+ Potential : [ 5.0, 0.19]
+ Convolutions : [ 76.6, 2.9]
+ Linear Algebra : [ 0.3, 9.77E-03]
+ Other : [ 6.6, 0.24]
+ Total : [ 99.2, 3.7]
+ Categories: #Ordered by time consumption
+ Precondition:
+ Data : [ 46.4, 1.7]
+ Class : Convolutions
+ Info : OpenCL ported
+ Rho_comput:
+ Data : [ 15.3, 0.57]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyLocPotKin:
+ Data : [ 14.9, 0.56]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyProj:
+ Data : [ 5.9, 0.22]
+ Class : Other
+ Info : RMA pattern
+ Init to Zero:
+ Data : [ 5.7, 0.21]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Exchange-Correlation:
+ Data : [ 5.0, 0.19]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ PSolver Computation:
+ Data : [ 1.6, 6.09E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Array allocations:
+ Data : [ 1.5, 5.52E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Routine Profiling:
+ Data : [ 1.0, 3.83E-02]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Diis:
+ Data : [ 0.7, 2.46E-02]
+ Class : Other
+ Info : Other
+ Vector copy:
+ Data : [ 0.5, 2.04E-02]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.3, 9.68E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Chol_comput:
+ Data : [ 0.3, 9.62E-03]
+ Class : Linear Algebra
+ Info : ALLReduce orbs
+ Un-TransSwitch:
+ Data : [ 0.0, 2.82E-04]
+ Class : Other
+ Info : RMA pattern
+ LagrM_comput:
+ Data : [ 0.0, 1.43E-04]
+ Class : Linear Algebra
+ Info : DGEMM
+ Pot_after_comm:
+ Data : [ 0.0, 8.58E-05]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 6.18E-05]
+ Class : Communications
+ Info : AllGathrv grid
+ LAST: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 6.1, 1.45E-02]
+ Communications : [ 0.0, 2.96E-05]
+ BLAS-LAPACK : [ 0.4, 1.00E-03]
+ PS Computation : [ 5.3, 1.27E-02]
+ Potential : [ 7.1, 1.70E-02]
+ Convolutions : [ 62.8, 0.15]
+ Other : [ 8.0, 1.91E-02]
+ Finalization : [ 1.0, 2.35E-03]
+ Total : [ 90.9, 0.24]
+ Categories: #Ordered by time consumption
+ Rho_comput:
+ Data : [ 43.2, 0.10]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyLocPotKin:
+ Data : [ 19.7, 4.69E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyProj:
+ Data : [ 8.0, 1.91E-02]
+ Class : Other
+ Info : RMA pattern
+ Exchange-Correlation:
+ Data : [ 7.1, 1.70E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ PSolver Computation:
+ Data : [ 5.3, 1.27E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Array allocations:
+ Data : [ 3.1, 7.26E-03]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Init to Zero:
+ Data : [ 1.3, 3.14E-03]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Routine Profiling:
+ Data : [ 1.2, 2.92E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Forces:
+ Data : [ 1.0, 2.35E-03]
+ Class : Finalization
+ Info : Miscellaneous
+ Vector copy:
+ Data : [ 0.5, 1.21E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.4, 9.73E-04]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Lapack (dsy-ssy-che-zhe)eev:
+ Data : [ 0.0, 2.93E-05]
+ Class : BLAS-LAPACK
+ Info : Lapack Eigenvalue Problem
+ Allreduce, Small Size:
+ Data : [ 0.0, 2.24E-05]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ Un-TransSwitch:
+ Data : [ 0.0, 1.31E-05]
+ Class : Other
+ Info : RMA pattern
+ Pot_after_comm:
+ Data : [ 0.0, 7.87E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 4.77E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Large Size:
+ Data : [ 0.0, 2.38E-06]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ SUMMARY: # % , Time (s)
+ INIT : [ 14.4, 0.67]
+ WFN_OPT : [ 80.4, 3.7]
+ LAST : [ 5.1, 0.24]
+ Total : [ 100.0, 4.6]
+ Routines timing and number of calls:
+ - Main_program: [ 5.32, 1, ~*]
+ Subroutines:
+ - process_run (id="posinp"): [ 4.64, 1, 87.16%*]
+ Subroutines:
+ - bigdft_state: [ 4.64, 1, 99.93%*]
+ Subroutines:
+ - quantum_mechanical_state: [ 4.64, 1, 99.93%*]
+ Subroutines:
+ - cluster: [ 4.64, 1, 99.91%]
+ Subroutines:
+ - preconditionall2: [ 1.80, 11, 38.70%]
+ Subroutines:
+ - precondition_preconditioner: [ 0.220, 55, 12.22%]
+ Subroutines:
+ - segment_invert: [ 0.168, 55, 76.26%]
+ - calculate_rmr_new: [ 2.570E-02, 330, 1.43%]
+ - finalise_precond_residue: [ 2.132E-03, 55, 0.12%]
+ - LocalHamiltonianApplication: [ 0.698, 12, 15.04%]
+ Subroutines:
+ - psir_to_vpsi: [ 2.625E-02, 60, 3.76%]
+ Subroutines:
+ - apply_potential_lr_nobounds: [ 2.219E-02, 60, 84.55%]
+ - orbital_basis_associate: [ 7.479E-04, 12, 0.11%]
+ - input_wf: [ 0.409, 1, 8.81%]
+ Subroutines:
+ - LocalHamiltonianApplication: [ 7.904E-02, 1, 19.32%]
+ Subroutines:
+ - psir_to_vpsi: [ 3.636E-03, 8, 4.60%]
+ Subroutines:
+ - apply_potential_lr_nobounds: [ 3.101E-03, 8, 85.28%]
+ - orbital_basis_associate: [ 6.398E-05, 1, 0.08%]
+ - updatePotential: [ 4.059E-02, 1, 9.92%]
+ Subroutines:
+ - XC_potential: [ 2.501E-02, 1, 61.62%]
+ Subroutines:
+ - xc_energy_new: [ 1.806E-02, 1, 72.22%]
+ Subroutines:
+ - xc_getvxc: [ 1.696E-02, 1, 93.92%]
+ - Electrostatic_Solver: [ 1.449E-02, 1, 35.69%]
+ Subroutines:
+ - apply_kernel: [ 1.363E-02, 1, 94.06%]
+ Subroutines:
+ - G_PoissonSolver: [ 8.244E-03, 1, 60.48%]
+ - daub_to_isf: [ 2.897E-02, 8, 7.08%]
+ - LDiagHam: [ 6.429E-03, 1, 1.57%]
+ - NonLocalHamiltonianApplication: [ 1.024E-03, 1, 0.25%]
+ Subroutines:
+ - atom_projector: [ 4.064E-04, 2, 39.69%]
+ Subroutines:
+ - crtproj: [ 2.946E-04, 2, 72.49%]
+ - orbital_basis_associate: [ 6.742E-05, 1, 6.58%]
+ - local_potential_dimensions: [ 1.679E-04, 3, 0.04%]
+ - check_linear_and_create_Lzd: [ 1.456E-04, 1, 0.04%]
+ - deallocate_work_arrays_sumrho: [ 9.347E-05, 1, 0.02%]
+ - initialize_work_arrays_sumrho: [ 8.117E-05, 1, 0.02%]
+ - full_local_potential: [ 5.719E-05, 1, 0.01%]
+ - SynchronizeHamiltonianApplication: [ 1.581E-05, 1, 0.00%]
+ - XC_potential: [ 0.271, 12, 5.85%]
+ Subroutines:
+ - xc_energy_new: [ 0.203, 12, 74.96%]
+ Subroutines:
+ - xc_getvxc: [ 0.192, 12, 94.59%]
+ - NonLocalHamiltonianApplication: [ 0.264, 12, 5.68%]
+ Subroutines:
+ - atom_projector: [ 0.215, 24, 81.36%]
+ Subroutines:
+ - crtproj: [ 0.210, 24, 97.60%]
+ - orbital_basis_associate: [ 8.614E-04, 12, 0.33%]
+ - system_initialization: [ 0.232, 1, 5.01%]
+ Subroutines:
+ - pkernel_set: [ 0.140, 1, 60.41%]
+ Subroutines:
+ - mpi_environment_set: [ 1.664E-05, 1, 0.01%]
+ - createWavefunctionsDescriptors: [ 4.054E-02, 1, 17.48%]
+ Subroutines:
+ - fill_logrid: [ 4.001E-02, 2, 98.69%]
+ - segkeys: [ 1.182E-04, 2, 0.29%]
+ - num_segkeys: [ 6.389E-05, 2, 0.16%]
+ - createProjectorsArrays: [ 1.485E-03, 1, 0.64%]
+ Subroutines:
+ - localize_projectors: [ 3.335E-04, 1, 22.46%]
+ Subroutines:
+ - fill_logrid: [ 1.286E-04, 4, 38.55%]
+ - num_segkeys: [ 8.524E-05, 4, 25.56%]
+ - set_wfd_to_wfd: [ 1.761E-04, 2, 11.86%]
+ Subroutines:
+ - init_tolr: [ 1.035E-04, 2, 58.79%]
+ - fill_logrid: [ 1.316E-04, 4, 8.87%]
+ - segkeys: [ 1.288E-04, 4, 8.68%]
+ - transform_keyglob_to_keygloc: [ 9.758E-05, 4, 6.57%]
+ - allocate_arrays: [ 7.538E-05, 1, 5.08%]
+ - gaussian_basis_from_psp: [ 4.477E-05, 1, 3.01%]
+ - nullify_structure: [ 1.484E-05, 1, 1.00%]
+ - orbital_basis_associate: [ 6.310E-05, 1, 0.03%]
+ - mpi_environment_set: [ 1.863E-05, 1, 0.01%]
+ - daub_to_isf: [ 0.221, 60, 4.77%]
+ - Electrostatic_Solver: [ 0.114, 12, 2.46%]
+ Subroutines:
+ - apply_kernel: [ 9.978E-02, 12, 87.53%]
+ Subroutines:
+ - G_PoissonSolver: [ 6.446E-02, 12, 64.60%]
+ - kswfn_post_treatments: [ 8.168E-02, 1, 1.76%]
+ Subroutines:
+ - daub_to_isf: [ 1.678E-02, 5, 20.54%]
+ - calculate_dipole_moment: [ 1.566E-02, 1, 19.17%]
+ - Electrostatic_Solver: [ 8.690E-03, 1, 10.64%]
+ Subroutines:
+ - apply_kernel: [ 8.151E-03, 1, 93.80%]
+ Subroutines:
+ - G_PoissonSolver: [ 7.398E-03, 1, 90.76%]
+ - calculate_forces: [ 3.074E-03, 1, 3.76%]
+ Subroutines:
+ - nonlocal_forces: [ 2.175E-03, 1, 70.76%]
+ Subroutines:
+ - atom_projector: [ 1.624E-03, 8, 74.66%]
+ Subroutines:
+ - crtproj: [ 1.333E-03, 8, 82.07%]
+ - local_forces: [ 7.903E-04, 1, 25.71%]
+ - rhocore_forces: [ 1.516E-05, 1, 0.49%]
+ - deallocate_work_arrays_sumrho: [ 9.532E-05, 1, 0.12%]
+ - orbital_basis_associate: [ 7.762E-05, 1, 0.10%]
+ - initialize_work_arrays_sumrho: [ 5.271E-05, 1, 0.06%]
+ - IonicEnergyandForces: [ 1.707E-02, 1, 0.37%]
+ Subroutines:
+ - Electrostatic_Solver: [ 1.460E-02, 1, 85.53%]
+ Subroutines:
+ - apply_kernel: [ 1.404E-02, 1, 96.14%]
+ Subroutines:
+ - G_PoissonSolver: [ 1.231E-02, 1, 87.65%]
+ - vdwcorrection_calculate_energy: [ 2.045E-05, 1, 0.12%]
+ - vdwcorrection_calculate_forces: [ 1.522E-05, 1, 0.09%]
+ - createEffectiveIonicPotential: [ 1.051E-02, 1, 0.23%]
+ Subroutines:
+ - createIonicPotential: [ 1.046E-02, 1, 99.53%]
+ Subroutines:
+ - Electrostatic_Solver: [ 8.810E-03, 1, 84.23%]
+ Subroutines:
+ - apply_kernel: [ 8.165E-03, 1, 92.68%]
+ Subroutines:
+ - G_PoissonSolver: [ 7.338E-03, 1, 89.87%]
+ - timing_dump_results: [ 1.633E-03, 2, 0.04%]
+ - deallocate_work_arrays_sumrho: [ 1.233E-03, 12, 0.03%]
+ - full_local_potential: [ 9.546E-04, 12, 0.02%]
+ - initialize_work_arrays_sumrho: [ 7.926E-04, 12, 0.02%]
+ - SynchronizeHamiltonianApplication: [ 2.900E-04, 12, 0.01%]
+ - interaction_multipoles_ions: [ 6.034E-05, 1, 0.00%]
+ - ionic_energy_of_external_charges: [ 3.196E-05, 1, 0.00%]
+ - potential_from_charge_multipoles: [ 2.560E-05, 1, 0.00%]
+ - timing_dump_results: [ 7.589E-04, 1, 0.02%]
+ - bigdft_init: [ 0.622, 1, 11.70%]
+ Subroutines:
+ - mpi_environment_set: [ 2.431E-05, 1, 0.00%]
+ - run_objects_init: [ 5.780E-02, 1, 1.09%]
+ Subroutines:
+ - set_run_objects: [ 3.664E-02, 1, 63.39%]
+ Subroutines:
+ - inputs_from_dict: [ 3.654E-02, 1, 99.73%]
+ Subroutines:
+ - input_keys_dump: [ 1.454E-02, 1, 39.78%]
+ - astruct_set_from_dict: [ 1.057E-02, 1, 28.93%]
+ - input_keys_fill_all: [ 8.701E-03, 1, 23.81%]
+ Subroutines:
+ - input_keys_init: [ 4.763E-03, 1, 54.74%]
+ - PS_input_dict: [ 8.362E-04, 1, 9.61%]
+ - psp_dict_fill_all: [ 2.123E-04, 1, 0.58%]
+ - psp_dict_analyse: [ 2.086E-04, 1, 0.57%]
+ - allocateBasicArraysInputLin: [ 7.747E-05, 1, 0.21%]
+ - atomic_data_set_from_dict: [ 6.139E-05, 1, 0.17%]
+ - kpt_input_analyse: [ 5.144E-05, 1, 0.14%]
+ - atomic_gamma_from_dict: [ 2.521E-05, 1, 0.07%]
+ - occupation_set_from_dict: [ 2.358E-05, 1, 0.06%]
+ - input_analyze: [ 1.802E-05, 1, 0.05%]
+ - read_n_orbitals: [ 1.452E-05, 1, 0.04%]
+ - astruct_file_merge_to_dict: [ 2.062E-02, 1, 35.68%]
+ - read_input_dict_from_files: [ 3.508E-05, 1, 0.06%]
+ CPU parallelism:
+ MPI tasks : 1
+ OMP threads : 8
+ Report timestamp : 2016-12-02 09:06:19.787
diff --git a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py
index 580d9871324660219edaa33dbd27d8bdc2bda215..1fa2a039467148c8d09f3ca3e50ae11323b87ef2 100644
--- a/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py
+++ b/parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/run_tests.py
@@ -59,6 +59,14 @@ class TestSinglePoint(unittest.TestCase):
result = self.results["program_name"]
self.assertEqual(result, "BigDFT")
+ def test_program_version(self):
+ result = self.results["program_version"]
+ self.assertEqual(result, "1.8")
+
+ def test_program_basis_set_type(self):
+ result = self.results["program_basis_set_type"]
+ self.assertEqual(result, "real-space grid")
+
def test_simulation_cell(self):
result = self.results["simulation_cell"]
expected_result = convert_unit(np.array(
@@ -70,17 +78,13 @@ class TestSinglePoint(unittest.TestCase):
), "angstrom")
self.assertTrue(np.array_equal(result, expected_result))
- # def test_configuration_periodic_dimensions(self):
- # result = self.results["configuration_periodic_dimensions"]
- # self.assertTrue(np.array_equal(result, np.array([False, False, False])))
-
- def test_program_version(self):
- result = self.results["program_version"]
- self.assertEqual(result, "1.8")
+ def test_configuration_periodic_dimensions(self):
+ result = self.results["configuration_periodic_dimensions"]
+ self.assertTrue(np.array_equal(result, np.array([False, False, False])))
- # def test_xc_functional(self):
- # result = self.results["XC_functional"]
- # self.assertEqual(result, "1.0*MGGA_C_TPSS+1.0*MGGA_X_TPSS")
+ def test_xc_functional(self):
+ result = self.results["XC_functional"]
+ self.assertEqual(result, "1.0*LDA_XC_TETER93")
def test_atom_labels(self):
atom_labels = self.results["atom_labels"]
@@ -105,9 +109,13 @@ class TestSinglePoint(unittest.TestCase):
result = self.results["electronic_structure_method"]
self.assertEqual(result, "DFT")
- # def test_total_charge(self):
- # charge = self.results["total_charge"]
- # self.assertEqual(charge, 0)
+ def test_total_charge(self):
+ charge = self.results["total_charge"]
+ self.assertEqual(charge, 0)
+
+ def test_number_of_spin_channels(self):
+ result = self.results["number_of_spin_channels"]
+ self.assertEqual(result, 1)
# def test_energy_total(self):
# result = self.results["energy_total"]
@@ -143,14 +151,13 @@ class TestSinglePoint(unittest.TestCase):
# ]), "hartree")
# self.assertTrue(np.array_equal(np.array([[result[0]], [result[-1]]]), expected_result))
- # def test_scf_max_iteration(self):
- # result = self.results["scf_max_iteration"]
- # self.assertEqual(result, 50)
-
- # def test_scf_threshold_energy_change(self):
- # result = self.results["scf_threshold_energy_change"]
- # self.assertEqual(result, convert_unit(1.00E-06, "hartree"))
+ def test_scf_max_iteration(self):
+ result = self.results["scf_max_iteration"]
+ self.assertEqual(result, 50)
+ def test_scf_threshold_energy_change(self):
+ result = self.results["scf_threshold_energy_change"]
+ self.assertEqual(result, convert_unit(1.0E-04, "hartree"))
# def test_scf_dft_number_of_iterations(self):
# result = self.results["number_of_scf_iterations"]
@@ -177,33 +184,6 @@ class TestSinglePoint(unittest.TestCase):
# self.assertEqual(kind["method_atom_kind_atom_number"][0], 1)
# self.assertEqual(kind["method_atom_kind_label"][0], "H")
- # def test_section_method_basis_set(self):
- # kind = self.results["section_method_basis_set"][0]
- # self.assertEqual(kind["method_basis_set_kind"][0], "wavefunction")
- # self.assertTrue(np.array_equal(kind["mapping_section_method_basis_set_cell_associated"][0], 0))
-
- # def test_number_of_spin_channels(self):
- # result = self.results["number_of_spin_channels"]
- # self.assertEqual(result, 1)
-
- # def test_simulation_cell(self):
- # cell = self.results["simulation_cell"]
- # n_vectors = cell.shape[0]
- # n_dim = cell.shape[1]
- # self.assertEqual(n_vectors, 3)
- # self.assertEqual(n_dim, 3)
- # expected_cell = convert_unit(np.array([[15.1178, 0, 0], [0, 15.1178, 0], [0, 0, 15.1178]]), "bohr")
- # self.assertTrue(np.array_equal(cell, expected_cell))
-
- # def test_basis_set_cell_dependent(self):
- # kind = self.results["basis_set_cell_dependent_kind"]
- # name = self.results["basis_set_cell_dependent_name"]
- # cutoff = self.results["basis_set_planewave_cutoff"]
-
- # self.assertEqual(kind, "plane_waves")
- # self.assertEqual(name, "PW_70.0")
- # self.assertEqual(cutoff, convert_unit(70.00000, "rydberg"))
-
#===============================================================================
if __name__ == '__main__':
diff --git a/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py b/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
index d2bbd7a3694d00e990bb27299dd44d5cdc1779be..45de8546233d8a3c8dec268ae6abfde7ec1d69e5 100644
--- a/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
+++ b/parser/parser-big-dft/bigdftparser/versions/bigdft18/mainparser.py
@@ -22,7 +22,9 @@ class BigDFTMainParser(AbstractBaseParser):
"Version Number": lambda x: self.backend.addValue("program_version", x),
"Atomic structure": self.atomic_structure,
"Sizes of the simulation domain": self.simulation_domain,
- # "Atomic Forces (Ha/Bohr)": self.atomic_structure
+ "Atomic System Properties": self.atomic_system_properties,
+ "dft": self.dft,
+ "DFT parameters": self.dft_parameters,
}
def parse(self):
@@ -41,6 +43,7 @@ class BigDFTMainParser(AbstractBaseParser):
section_method_id = self.backend.openSection("section_method")
self.backend.addValue("program_name", "BigDFT")
self.backend.addValue("electronic_structure_method", "DFT")
+ self.backend.addValue("program_basis_set_type", "real-space grid")
loader = Loader(fin)
generator = self.generate_root_nodes(loader)
@@ -81,16 +84,18 @@ class BigDFTMainParser(AbstractBaseParser):
value = loader.construct_scalar(value)
yield (key, value)
+ #===========================================================================
+ # The following functions handle the different sections in the output
def scf(self, scf):
"""Parse the SCF loop information.
"""
print("Moi")
return
- def atomic_structure(self, structure):
+ def atomic_structure(self, value):
np_positions = []
np_labels = []
- positions = structure["Positions"]
+ positions = value["Positions"]
for position in positions:
np_positions.append(*position.values())
np_labels.append(*position.keys())
@@ -98,8 +103,106 @@ class BigDFTMainParser(AbstractBaseParser):
np_labels = np.array(np_labels)
self.backend.addArrayValues("atom_positions", np_positions, unit="angstrom")
self.backend.addArrayValues("atom_labels", np_labels)
- self.backend.addValue("number_of_atoms", np_labels.size)
def simulation_domain(self, value):
simulation_cell = np.diag(value["Angstroem"])
self.backend.addArrayValues("simulation_cell", simulation_cell, unit="angstrom")
+
+ def atomic_system_properties(self, value):
+ # Number of atoms
+ n_atoms = value["Number of atoms"]
+ self.backend.addValue("number_of_atoms", n_atoms)
+
+ # Periodicity
+ boundary = value["Boundary Conditions"]
+ if boundary == "Free":
+ periodic_dimensions = np.array([False, False, False])
+ elif boundary == "Periodic":
+ periodic_dimensions = np.array([True, True, True])
+ elif boundary == "Surface":
+ periodic_dimensions = np.array([True, False, True])
+ else:
+ raise Exception("Unknown boundary condtions.")
+ self.backend.addArrayValues("configuration_periodic_dimensions", periodic_dimensions)
+
+ def dft(self, value):
+ # Total_charge
+ charge = value["qcharge"]
+ self.backend.addValue("total_charge", charge)
+
+ # SCF options
+ max_iter = value["itermax"]
+ self.backend.addValue("scf_max_iteration", max_iter)
+ energy_gradient = value["gnrm_cv"]
+ self.backend.addRealValue("scf_threshold_energy_change", energy_gradient, unit="hartree")
+
+ # Spin channels
+ n_spin = value["nspin"]
+ self.backend.addValue("number_of_spin_channels", n_spin)
+
+ def dft_parameters(self, value):
+ # XC functional
+ exchange_settings = value["eXchange Correlation"]
+ xc_id = exchange_settings["XC ID"]
+
+ # LibXC codes
+ if xc_id < 0:
+ mapping = {
+ 1: ["LDA_XC_TETER93"],
+ 2: ["LDA_C_PZ"],
+ }
+
+ # ABINIT codes, see
+ # http://www.tddft.org/programs/octopus/wiki/index.php/Developers_Manual:ABINIT
+ # and
+ # http://www.abinit.org/doc/helpfiles/for-v8.0/input_variables/html_automatically_generated/varbas.html#ixc
+ else:
+ mapping = {
+ 1: ["LDA_XC_TETER93"],
+ 2: ["LDA_C_PZ"],
+ # 3: Unknown
+ 4: ["LDA_C_WIGNER"],
+ 5: ["LDA_C_HL"],
+ 6: ["LDA_C_XALPHA"],
+ # 7: ["LDA_XC_PW"], # Not really sure...
+ # 8: ["LDA_X_PW"], # Not really sure...
+ # 9: ["LDA_X_PW", "LDA_C_RPA"], # Not really sure...
+ # 10: Internal
+ 11: ["GGA_C_PBE", "GGA_X_PBE"],
+ 12: ["GGA_X_PBE"],
+ # 13: ["GGA_C_PBE","GGA_X_LB"], # Not really sure...
+ # 14: ["GGA_C_PBE","GGA_X_PBE_R"], # Not really sure...
+ 15: ["GGA_C_PBE", "GGA_X_RPBE"],
+ 16: ["GGA_XC_HCTH_93"],
+ 17: ["GGA_XC_HCTH_120"],
+ # 20: Unknown
+ # 21: Unknown
+ # 22: Unknown
+ 23: ["GGA_X_WC"],
+ 24: ["GGA_X_C09X"],
+ # 25: Internal
+ 26: ["GGA_XC_HCTH_147"],
+ 27: ["GGA_XC_HCTH_147"],
+ # 28: Internal
+ 40: ["HF_X"],
+ 41: ["HYB_GGA_XC_PBEH"],
+ 42: ["HYB_GGA_XC_PBE0_13"],
+ }
+
+ # Create the XC sections and a summary
+ xc = mapping.get(xc_id)
+ if xc is None:
+ raise Exception("Unknown XC functional.")
+ sorted_xc = sorted(xc)
+ summary = ""
+ n_names = len(sorted_xc)
+ for i_name, name in enumerate(sorted_xc):
+ weight = 1.0
+ xc_id = self.backend.openSection("section_XC_functionals")
+ self.backend.addValue("XC_functional_name", name)
+ self.backend.addValue("XC_functional_weight", weight)
+ self.backend.closeSection("section_XC_functionals", xc_id)
+ summary += "{}*{}".format(weight, name)
+ if i_name+1 != n_names:
+ summary += "_"
+ self.backend.addValue("XC_functional", summary)
diff --git a/src/main/scala/eu/nomad_lab/parsers/NWChemParser.scala b/src/main/scala/eu/nomad_lab/parsers/BigDFTParser.scala
similarity index 51%
rename from src/main/scala/eu/nomad_lab/parsers/NWChemParser.scala
rename to src/main/scala/eu/nomad_lab/parsers/BigDFTParser.scala
index 7ce6d9f20de3212e7c89b1ad8fa2dc5d17b1667b..bdc7bca60476b70ecaddd813cb68df8123be6dc2 100644
--- a/src/main/scala/eu/nomad_lab/parsers/NWChemParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/BigDFTParser.scala
@@ -21,14 +21,35 @@ object BigDFTParser extends SimpleExternalParserGenerator(
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
- mainFileRe = """ Northwest Computational Chemistry Package \(NWChem\) \d+\.\d+
- ------------------------------------------------------
-
-
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland, WA 99352""".r,
- cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/nwchem/parser/parser-nwchem/nwchemparser/scalainterface.py",
+ mainFileRe = """---
+ Code logo:
+ "__________________________________ A fast and precise DFT wavelet code
+ | | | | | |
+ | | | | | | BBBB i gggggg
+ |_____|_____|_____|_____|_____| B B g
+ | | : | : | | | B B i g
+ | |-0+--|-0+--| | | B B i g g
+ |_____|__:__|__:__|_____|_____|___ BBBBB i g g
+ | : | | | : | | B B i g g
+ |--+0-| | |-0+--| | B B iiii g g
+ |__:__|_____|_____|__:__|_____| B B i g g
+ | | : | : | | | B BBBB i g g
+ | |-0+--|-0+--| | | B iiiii gggggg
+ |_____|__:__|__:__|_____|_____|__BBBBB
+ | | | | : | | TTTTTTTTT
+ | | | |--+0-| | DDDDDD FFFFF T
+ |_____|_____|_____|__:__|_____| D D F TTTT T
+ | | | | : | |D D F T T
+ | | | |--+0-| |D D FFFF T T
+ |_____|_____|_____|__:__|_____|D___ D F T T
+ | | | : | | |D D F TTTTT
+ | | |--+0-| | | D D F T T
+ |_____|_____|__:__|_____|_____| D F T T
+ | | | | | | D T T
+ | | | | | | DDDDDD F TTTT
+ |_____|_____|_____|_____|_____|______ www.bigdft.org "
+""".r,
+ cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/big-dft/parser/parser-big-dft/bigdftparser/scalainterface.py",
"${mainFilePath}"),
cmdCwd = "${mainFilePath}/..",
resList = Seq(
diff --git a/test/examples/single_point/forces_posinp.xyz b/test/examples/single_point/forces_posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..f153ad07ad4d436b235cb2ef0972f7aead52d2af
--- /dev/null
+++ b/test/examples/single_point/forces_posinp.xyz
@@ -0,0 +1,7 @@
+ 2 angstroemd0 -1.98834837256869790E+01 (Ha) Geometry + metaData forces
+ free
+ N 0.00000000000000000E+00 0.00000000000000000E+00 0.00000000000000000E+00
+ N 0.00000000000000000E+00 0.00000000000000000E+00 1.11498999595642090E+00
+ forces
+N -1.69406589450860068E-21 -3.38813178901720136E-21 5.67055414067736407E-02
+N 1.69406589450860068E-21 3.38813178901720136E-21 -5.67055414067736407E-02
diff --git a/test/examples/single_point/input_minimal.yaml b/test/examples/single_point/input_minimal.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..f468acac1a41b1bef200c71027b601610a130937
--- /dev/null
+++ b/test/examples/single_point/input_minimal.yaml
@@ -0,0 +1,16 @@
+ #---------------------------------------------------------------------- Minimal input file
+ #This file indicates the minimal set of input variables which has to be given to perform
+ #the run. The code would produce the same output if this file is used as input.
+ posinp:
+ units: angstroem
+ positions:
+ - N: [0.0, 0.0, 0.0]
+ - N: [0.0, 0.0, 1.114989995956421]
+ properties:
+ format: xyz
+ source: posinp.xyz
+ psolver:
+ environment:
+ gammaS: water
+ alphaS: water
+ betaV: water
diff --git a/test/examples/single_point/output.out b/test/examples/single_point/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..0279db2fc876fd0bfed2cb6ba3c31246b4b4521c
--- /dev/null
+++ b/test/examples/single_point/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
diff --git a/test/examples/single_point/posinp.xyz b/test/examples/single_point/posinp.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..8d7121b05ee67690f5bc0c1b1acc2308488e51ef
--- /dev/null
+++ b/test/examples/single_point/posinp.xyz
@@ -0,0 +1,4 @@
+2 angstroem
+free
+N 0. 0. 0.
+N 0. 0. 1.11499
diff --git a/test/examples/single_point/time.yaml b/test/examples/single_point/time.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..288b4be2b779e715164523ba2fe90c956d1c8837
--- /dev/null
+++ b/test/examples/single_point/time.yaml
@@ -0,0 +1,442 @@
+---
+ INIT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 12.0, 7.98E-02]
+ Communications : [ 0.0, 2.48E-05]
+ BLAS-LAPACK : [ 0.8, 5.23E-03]
+ PS Computation : [ 36.8, 0.25]
+ Potential : [ 6.5, 4.32E-02]
+ Convolutions : [ 12.6, 8.43E-02]
+ Other : [ 0.1, 8.41E-04]
+ Initialization : [ 6.8, 4.52E-02]
+ Total : [ 75.6, 0.67]
+ Categories: #Ordered by time consumption
+ PSolver Kernel Creation:
+ Data : [ 21.1, 0.14]
+ Class : PS Computation
+ Info : ISF operations and creation of the kernel
+ PSolver Computation:
+ Data : [ 15.6, 0.10]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Init to Zero:
+ Data : [ 8.5, 5.65E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ ApplyLocPotKin:
+ Data : [ 6.9, 4.61E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Exchange-Correlation:
+ Data : [ 6.5, 4.32E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ wavefunction:
+ Data : [ 6.0, 4.03E-02]
+ Class : Initialization
+ Info : Miscellaneous
+ Rho_comput:
+ Data : [ 5.7, 3.82E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Array allocations:
+ Data : [ 2.3, 1.51E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.8, 5.23E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Vector copy:
+ Data : [ 0.6, 4.20E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Routine Profiling:
+ Data : [ 0.6, 4.02E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ CrtLocPot:
+ Data : [ 0.3, 2.16E-03]
+ Class : Initialization
+ Info : Miscellaneous
+ CrtDescriptors:
+ Data : [ 0.3, 1.85E-03]
+ Class : Initialization
+ Info : RMA Pattern
+ Input_comput:
+ Data : [ 0.1, 8.84E-04]
+ Class : Initialization
+ Info : Miscellaneous
+ ApplyProj:
+ Data : [ 0.1, 6.82E-04]
+ Class : Other
+ Info : RMA pattern
+ ionic_energy:
+ Data : [ 0.0, 8.49E-05]
+ Class : Other
+ Info : Miscellaneous
+ calc_bounds:
+ Data : [ 0.0, 3.67E-05]
+ Class : Other
+ Info : Miscellaneous
+ Un-TransSwitch:
+ Data : [ 0.0, 3.05E-05]
+ Class : Other
+ Info : RMA pattern
+ Allreduce, Large Size:
+ Data : [ 0.0, 1.79E-05]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ Pot_after_comm:
+ Data : [ 0.0, 7.39E-06]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.01E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Small Size:
+ Data : [ 0.0, 1.91E-06]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ WFN_OPT: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 12.4, 0.28]
+ Communications : [ 0.0, 5.39E-05]
+ BLAS-LAPACK : [ 0.4, 9.48E-03]
+ PS Computation : [ 19.5, 0.44]
+ Potential : [ 17.5, 0.40]
+ Convolutions : [ 37.8, 0.85]
+ Linear Algebra : [ 0.4, 8.92E-03]
+ Other : [ 10.0, 0.23]
+ Total : [ 98.0, 2.3]
+ Categories: #Ordered by time consumption
+ PSolver Computation:
+ Data : [ 19.5, 0.44]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Exchange-Correlation:
+ Data : [ 17.5, 0.40]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ ApplyLocPotKin:
+ Data : [ 14.2, 0.32]
+ Class : Convolutions
+ Info : OpenCL ported
+ Rho_comput:
+ Data : [ 12.8, 0.29]
+ Class : Convolutions
+ Info : OpenCL ported
+ Precondition:
+ Data : [ 10.8, 0.24]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyProj:
+ Data : [ 9.0, 0.20]
+ Class : Other
+ Info : RMA pattern
+ Init to Zero:
+ Data : [ 6.2, 0.14]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ Array allocations:
+ Data : [ 2.6, 5.78E-02]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Routine Profiling:
+ Data : [ 2.1, 4.81E-02]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Vector copy:
+ Data : [ 1.5, 3.36E-02]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Diis:
+ Data : [ 1.0, 2.15E-02]
+ Class : Other
+ Info : Other
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.4, 9.48E-03]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Chol_comput:
+ Data : [ 0.4, 8.82E-03]
+ Class : Linear Algebra
+ Info : ALLReduce orbs
+ Un-TransSwitch:
+ Data : [ 0.0, 4.20E-04]
+ Class : Other
+ Info : RMA pattern
+ LagrM_comput:
+ Data : [ 0.0, 1.02E-04]
+ Class : Linear Algebra
+ Info : DGEMM
+ Pot_after_comm:
+ Data : [ 0.0, 8.58E-05]
+ Class : Other
+ Info : global_to_loca
+ Pot_commun:
+ Data : [ 0.0, 5.39E-05]
+ Class : Communications
+ Info : AllGathrv grid
+ LAST: # % , Time (s)
+ Classes:
+ Flib LowLevel : [ 12.9, 4.29E-02]
+ Communications : [ 0.0, 1.65E-05]
+ BLAS-LAPACK : [ 0.3, 9.79E-04]
+ PS Computation : [ 25.2, 8.39E-02]
+ Potential : [ 11.4, 3.80E-02]
+ Convolutions : [ 29.3, 9.75E-02]
+ Other : [ 7.0, 2.32E-02]
+ Finalization : [ 0.8, 2.72E-03]
+ Total : [ 87.0, 0.33]
+ Categories: #Ordered by time consumption
+ PSolver Computation:
+ Data : [ 25.2, 8.39E-02]
+ Class : PS Computation
+ Info : 3D SG_FFT and related operations
+ Rho_comput:
+ Data : [ 15.5, 5.17E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ ApplyLocPotKin:
+ Data : [ 13.8, 4.59E-02]
+ Class : Convolutions
+ Info : OpenCL ported
+ Exchange-Correlation:
+ Data : [ 11.4, 3.80E-02]
+ Class : Potential
+ Info : Operations needed to construct local XC potential
+ Init to Zero:
+ Data : [ 9.7, 3.22E-02]
+ Class : Flib LowLevel
+ Info : Memset of storage space
+ ApplyProj:
+ Data : [ 7.0, 2.32E-02]
+ Class : Other
+ Info : RMA pattern
+ Array allocations:
+ Data : [ 1.3, 4.20E-03]
+ Class : Flib LowLevel
+ Info : Heap storage allocation and associated profiling
+ Vector copy:
+ Data : [ 1.0, 3.38E-03]
+ Class : Flib LowLevel
+ Info : Memory copy of arrays (excluded allocations)
+ Routine Profiling:
+ Data : [ 0.9, 3.08E-03]
+ Class : Flib LowLevel
+ Info : Profiling performances for debugging
+ Forces:
+ Data : [ 0.8, 2.72E-03]
+ Class : Finalization
+ Info : Miscellaneous
+ Blas (d-s-c-z)GeMM:
+ Data : [ 0.3, 9.50E-04]
+ Class : BLAS-LAPACK
+ Info : Blas General Matrix-Matrix multiplications of any float type
+ Lapack (dsy-ssy-che-zhe)eev:
+ Data : [ 0.0, 2.93E-05]
+ Class : BLAS-LAPACK
+ Info : Lapack Eigenvalue Problem
+ Un-TransSwitch:
+ Data : [ 0.0, 1.26E-05]
+ Class : Other
+ Info : RMA pattern
+ Pot_after_comm:
+ Data : [ 0.0, 8.34E-06]
+ Class : Other
+ Info : global_to_loca
+ Allreduce, Small Size:
+ Data : [ 0.0, 5.96E-06]
+ Class : Communications
+ Info : Allreduce operations for less than 5 elements
+ Pot_commun:
+ Data : [ 0.0, 5.72E-06]
+ Class : Communications
+ Info : AllGathrv grid
+ Allreduce, Large Size:
+ Data : [ 0.0, 4.77E-06]
+ Class : Communications
+ Info : Allreduce operations for more than 5 elements
+ SUMMARY: # % , Time (s)
+ INIT : [ 20.4, 0.67]
+ WFN_OPT : [ 69.4, 2.3]
+ LAST : [ 10.2, 0.33]
+ Total : [ 100.0, 3.3]
+ Routines timing and number of calls:
+ - Main_program: [ 3.58, 1, ~*]
+ Subroutines:
+ - process_run (id="posinp"): [ 3.26, 1, 91.17%*]
+ Subroutines:
+ - bigdft_state: [ 3.26, 1, 100.12%*]
+ Subroutines:
+ - quantum_mechanical_state: [ 3.26, 1, 100.12%*]
+ Subroutines:
+ - cluster: [ 3.26, 1, 100.09%]
+ Subroutines:
+ - Electrostatic_Solver: [ 0.558, 11, 17.13%]
+ Subroutines:
+ - apply_kernel: [ 0.535, 11, 95.91%]
+ Subroutines:
+ - G_PoissonSolver: [ 0.455, 11, 84.96%]
+ - XC_potential: [ 0.450, 11, 13.80%]
+ Subroutines:
+ - xc_energy_new: [ 0.427, 11, 94.92%]
+ Subroutines:
+ - xc_getvxc: [ 0.403, 11, 94.38%]
+ - LocalHamiltonianApplication: [ 0.447, 11, 13.71%]
+ Subroutines:
+ - psir_to_vpsi: [ 9.405E-02, 55, 21.04%]
+ Subroutines:
+ - apply_potential_lr_bounds: [ 8.978E-02, 55, 95.46%]
+ - orbital_basis_associate: [ 7.953E-04, 11, 0.18%]
+ - input_wf: [ 0.418, 1, 12.83%]
+ Subroutines:
+ - updatePotential: [ 0.103, 1, 24.60%]
+ Subroutines:
+ - Electrostatic_Solver: [ 5.468E-02, 1, 53.09%]
+ Subroutines:
+ - apply_kernel: [ 5.267E-02, 1, 96.32%]
+ Subroutines:
+ - G_PoissonSolver: [ 3.807E-02, 1, 72.28%]
+ - XC_potential: [ 4.549E-02, 1, 44.17%]
+ Subroutines:
+ - xc_energy_new: [ 4.242E-02, 1, 93.25%]
+ Subroutines:
+ - xc_getvxc: [ 4.014E-02, 1, 94.63%]
+ - LocalHamiltonianApplication: [ 5.015E-02, 1, 12.00%]
+ Subroutines:
+ - psir_to_vpsi: [ 1.137E-02, 8, 22.66%]
+ Subroutines:
+ - apply_potential_lr_bounds: [ 1.082E-02, 8, 95.21%]
+ - orbital_basis_associate: [ 7.065E-05, 1, 0.14%]
+ - daub_to_isf: [ 2.794E-02, 8, 6.68%]
+ - LDiagHam: [ 6.435E-03, 1, 1.54%]
+ - NonLocalHamiltonianApplication: [ 1.053E-03, 1, 0.25%]
+ Subroutines:
+ - atom_projector: [ 3.907E-04, 2, 37.10%]
+ Subroutines:
+ - crtproj: [ 2.894E-04, 2, 74.06%]
+ - orbital_basis_associate: [ 1.072E-04, 1, 10.18%]
+ - check_linear_and_create_Lzd: [ 4.574E-04, 1, 0.11%]
+ - local_potential_dimensions: [ 1.878E-04, 3, 0.04%]
+ - initialize_work_arrays_sumrho: [ 1.139E-04, 1, 0.03%]
+ - deallocate_work_arrays_sumrho: [ 1.026E-04, 1, 0.02%]
+ - full_local_potential: [ 5.499E-05, 1, 0.01%]
+ - SynchronizeHamiltonianApplication: [ 1.723E-05, 1, 0.00%]
+ - preconditionall2: [ 0.332, 10, 10.17%]
+ Subroutines:
+ - precondition_preconditioner: [ 0.130, 50, 39.29%]
+ Subroutines:
+ - prec_diag: [ 0.110, 50, 84.45%]
+ - calculate_rmr_new: [ 2.244E-02, 300, 6.76%]
+ - compress_forstandard: [ 1.255E-02, 350, 3.78%]
+ - finalise_precond_residue: [ 1.630E-03, 50, 0.49%]
+ - NonLocalHamiltonianApplication: [ 0.249, 11, 7.65%]
+ Subroutines:
+ - atom_projector: [ 0.206, 22, 82.67%]
+ Subroutines:
+ - crtproj: [ 0.202, 22, 98.17%]
+ - orbital_basis_associate: [ 8.054E-04, 11, 0.32%]
+ - daub_to_isf: [ 0.194, 55, 5.95%]
+ - system_initialization: [ 0.172, 1, 5.27%]
+ Subroutines:
+ - pkernel_set: [ 0.151, 1, 88.06%]
+ Subroutines:
+ - mpi_environment_set: [ 2.242E-05, 1, 0.01%]
+ - createWavefunctionsDescriptors: [ 2.376E-03, 1, 1.38%]
+ Subroutines:
+ - fill_logrid: [ 7.696E-04, 2, 32.39%]
+ - segkeys: [ 1.330E-04, 2, 5.60%]
+ - num_segkeys: [ 9.318E-05, 2, 3.92%]
+ - createProjectorsArrays: [ 1.333E-03, 1, 0.78%]
+ Subroutines:
+ - localize_projectors: [ 2.997E-04, 1, 22.49%]
+ Subroutines:
+ - fill_logrid: [ 1.107E-04, 4, 36.95%]
+ - num_segkeys: [ 7.907E-05, 4, 26.38%]
+ - set_wfd_to_wfd: [ 1.624E-04, 2, 12.18%]
+ Subroutines:
+ - init_tolr: [ 9.017E-05, 2, 55.52%]
+ - fill_logrid: [ 1.071E-04, 4, 8.03%]
+ - segkeys: [ 9.435E-05, 4, 7.08%]
+ - transform_keyglob_to_keygloc: [ 8.347E-05, 4, 6.26%]
+ - allocate_arrays: [ 8.193E-05, 1, 6.15%]
+ - gaussian_basis_from_psp: [ 3.976E-05, 1, 2.98%]
+ - nullify_structure: [ 1.586E-05, 1, 1.19%]
+ - orbital_basis_associate: [ 6.494E-05, 1, 0.04%]
+ - mpi_environment_set: [ 2.481E-05, 1, 0.01%]
+ - kswfn_post_treatments: [ 0.116, 1, 3.56%]
+ Subroutines:
+ - Electrostatic_Solver: [ 4.715E-02, 1, 40.64%]
+ Subroutines:
+ - apply_kernel: [ 4.552E-02, 1, 96.55%]
+ Subroutines:
+ - G_PoissonSolver: [ 4.300E-02, 1, 94.47%]
+ - calculate_dipole_moment: [ 3.459E-02, 1, 29.82%]
+ - daub_to_isf: [ 1.472E-02, 5, 12.69%]
+ - calculate_forces: [ 3.505E-03, 1, 3.02%]
+ Subroutines:
+ - nonlocal_forces: [ 1.854E-03, 1, 52.88%]
+ Subroutines:
+ - atom_projector: [ 1.328E-03, 8, 71.65%]
+ Subroutines:
+ - crtproj: [ 1.035E-03, 8, 77.96%]
+ - local_forces: [ 1.516E-03, 1, 43.26%]
+ - rhocore_forces: [ 1.599E-05, 1, 0.46%]
+ - deallocate_work_arrays_sumrho: [ 1.125E-04, 1, 0.10%]
+ - orbital_basis_associate: [ 8.024E-05, 1, 0.07%]
+ - initialize_work_arrays_sumrho: [ 7.995E-05, 1, 0.07%]
+ - createEffectiveIonicPotential: [ 7.497E-02, 1, 2.30%]
+ Subroutines:
+ - createIonicPotential: [ 7.493E-02, 1, 99.95%]
+ Subroutines:
+ - Electrostatic_Solver: [ 6.942E-02, 1, 92.65%]
+ Subroutines:
+ - apply_kernel: [ 6.783E-02, 1, 97.72%]
+ Subroutines:
+ - G_PoissonSolver: [ 6.332E-02, 1, 93.35%]
+ - initialize_work_arrays_sumrho: [ 2.100E-03, 11, 0.06%]
+ - timing_dump_results: [ 1.678E-03, 2, 0.05%]
+ - deallocate_work_arrays_sumrho: [ 1.196E-03, 11, 0.04%]
+ - full_local_potential: [ 8.754E-04, 11, 0.03%]
+ - IonicEnergyandForces: [ 5.848E-04, 1, 0.02%]
+ Subroutines:
+ - vdwcorrection_calculate_energy: [ 2.333E-05, 1, 3.99%]
+ - vdwcorrection_calculate_forces: [ 1.490E-05, 1, 2.55%]
+ - SynchronizeHamiltonianApplication: [ 2.837E-04, 11, 0.01%]
+ - interaction_multipoles_ions: [ 1.270E-04, 1, 0.00%]
+ - ionic_energy_of_external_charges: [ 6.251E-05, 1, 0.00%]
+ - potential_from_charge_multipoles: [ 1.677E-05, 1, 0.00%]
+ - timing_dump_results: [ 7.465E-04, 1, 0.02%]
+ - bigdft_init: [ 0.267, 1, 7.47%]
+ Subroutines:
+ - mpi_environment_set: [ 2.551E-05, 1, 0.01%]
+ - run_objects_init: [ 4.769E-02, 1, 1.33%]
+ Subroutines:
+ - set_run_objects: [ 2.943E-02, 1, 61.72%]
+ Subroutines:
+ - inputs_from_dict: [ 2.937E-02, 1, 99.79%]
+ Subroutines:
+ - input_keys_dump: [ 1.510E-02, 1, 51.40%]
+ - input_keys_fill_all: [ 8.871E-03, 1, 30.20%]
+ Subroutines:
+ - input_keys_init: [ 4.788E-03, 1, 53.97%]
+ - PS_input_dict: [ 8.553E-04, 1, 9.64%]
+ - astruct_set_from_dict: [ 3.152E-03, 1, 10.73%]
+ - psp_dict_analyse: [ 2.099E-04, 1, 0.71%]
+ - psp_dict_fill_all: [ 2.004E-04, 1, 0.68%]
+ - allocateBasicArraysInputLin: [ 7.579E-05, 1, 0.26%]
+ - atomic_data_set_from_dict: [ 7.271E-05, 1, 0.25%]
+ - kpt_input_analyse: [ 4.459E-05, 1, 0.15%]
+ - atomic_gamma_from_dict: [ 2.605E-05, 1, 0.09%]
+ - occupation_set_from_dict: [ 2.500E-05, 1, 0.09%]
+ - input_analyze: [ 1.720E-05, 1, 0.06%]
+ - read_n_orbitals: [ 1.447E-05, 1, 0.05%]
+ - astruct_file_merge_to_dict: [ 1.775E-02, 1, 37.22%]
+ - read_input_dict_from_files: [ 3.546E-05, 1, 0.07%]
+ CPU parallelism:
+ MPI tasks : 1
+ OMP threads : 8
+ Report timestamp : 2016-11-11 13:02:26.902