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Commit aa6df075 authored by Lauri Himanen's avatar Lauri Himanen
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Support for most basic metainfos, some XC functionals now supported, adding... 

Support for most basic metainfos, some XC functionals now supported, adding more. Added proper scala integration.
parent c45a92f9
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parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/forces_posinp.xyz 0 → 100644
View file @ aa6df075
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
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/input_minimal.yaml 0 → 100644
View file @ aa6df075
#---------------------------------------------------------------------- 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
parser/parser-big-dft/bigdftparser/regtest/bigdft_1.8/periodicity/free/output.out 0 → 100644
View file @ aa6df075
---
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}