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Version : 5.4.2
Architecture : x86_64
Compiler version: GNU-14.3.0
Compiler flags : -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem <prefix>/include -I<prefix>/_build_env/include -fdebug-prefix-map=<prefix>/work=/usr/local/src/conda/siesta-5.4.2 -fdebug-prefix-map=<prefix>=/usr/local/src/conda-prefix -I<prefix>/lib -fallow-argument-mismatch -O3
Parallelisations: none
NetCDF support
NetCDF-4 support
Lua support
DFT-D3 support
Runtime information:
* Directory : /home/apolyukhin/Development/HPRO/examples/Diamond/aobasis
* Running in serial mode.
>> Start of run: 31-JAN-2026 22:37:41
***********************
* WELCOME TO SIESTA *
***********************
NOTE: Siesta V5 introduces some new defaults for basis-set generation
NOTE: which might lead to slightly different numerical results.
NOTE: Please see the manual for full details and compatibility measures.
reinit: Reading from standard input
reinit: Dumping input in INPUT_TMP.08556
************************** Dump of input data file ****************************
SystemName Diamond
SystemLabel siesta
NumberOfAtoms 2
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 6 C
%endblock ChemicalSpeciesLabel
LatticeConstant 3.567 Ang
%block LatticeVectors
0.0 0.5 0.5
0.5 0.0 0.5
0.5 0.5 0.0
%endblock LatticeVectors
AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.00 0.00 0.00 1
0.25 0.25 0.25 1
%endblock AtomicCoordinatesAndAtomicSpecies
PAO.BasisSize DZP
PAO.BasisType nodes
%block PAO.Basis
C 2
n=2 0 2
0.000 0.000
1.000 1.000
n=2 1 2 P
0.000 0.000
1.000 1.000
%endblock PAO.Basis
%block kgrid_Monkhorst_Pack
4 0 0 0.0
0 4 0 0.0
0 0 4 0.0
%endblock kgrid_Monkhorst_Pack
SolutionMethod diagon
OccupationFunction MP
ElectronicTemperature 0.0000 eV
MaxSCFIterations 300
MeshCutoff 320.0 Ry
DM.Tolerance 1.E-6
SCF.H.Converge F
UseSaveData F
DM.UseSaveDM F
SpinOrbit F
Diag.ParallelOverK T
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Diamond
reinit: -----------------------------------------------------------------------
reinit: System Label: siesta
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 6 Label: C
Ground state valence configuration (from tables): 2s02 2p02 3d00 4f00
---- Processing specs for species: C
Reading pseudopotential information in PSML from:
C.psml
PSML file version: 1.1
Using libxc ids: 101 130
GGA--PBE XC_GGA_X_PBE--XC_GGA_C_PBE pb
PSML uuid: 297821e0-be41-11e7-6802-e1ff7dfff095
---- Pseudopotential check for C
Pseudized shells:
2s( 2.00) rc: 1.20
2p( 2.00) rc: 1.26
Valence configuration for ps generation: 2s:2p: Total charge: 4.000000
C: adding empty (pol) shell: 3d
For C, standard SIESTA heuristics set lmxkb to 3
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
C pseudopotential only contains V_ls up to l=1 -- lmxkb reset.
<basis_specs>
===============================================================================
C Z= 6 Mass= 12.011 Charge= 0.17977+309
Lmxo=2 Lmxkb= 1 BasisType=nodes Semic=F
L=0 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=0 (2s)
splnorm: 0.15000
vcte: 40.000
rinn: -0.90000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
i=1 nzeta=2 polorb=1 (2p) (to be polarized perturbatively)
splnorm: 0.15000
vcte: 40.000
rinn: -0.90000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
L=2 Nsemic=0 Cnfigmx=3
i=1 nzeta=0 polorb=0 (3d) (perturbative polarization orbital) (from 2p)
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>
Using PAO.SplitTailNorm
atom: Called for C (Z = 6)
NOTE: C pseudopotential has channels up to l= 1
NOTE: PAOs with higher l will be generated with V_local
Maximum radius (at nrval) set to 50.00000 8518
read_vps: Pseudopotential generation method:
read_vps: ONCVPSP-3.Hamann's oncvpsp
Valence charge in pseudo generation: 4.00000
read_vps: Pseudopotential includes a core correction:
read_vps: Pseudo-core for xc-correction
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
xc_check: WARNING: Pseudopotential generated with GGA PBE functional
Got Vlocal (oncv-fit) from psml data
Choosing vlocal chloc cutoff: 4.122282
qtot up to nchloc: 4.00001153
atom: Maximum radius for chlocal: 4.12228
atom: Maximum radius for r*vlocal+2*Zval: 4.12228
Reading KB projs from C psml data
Using scalar-relativistic projectors in PSML file
PSML: Kleinman-Bylander projectors:
l= 0 rc= 1.219773 Ekb= 12.963096
l= 0 rc= 1.219773 Ekb= 0.771007
l= 1 rc= 1.278952 Ekb= -8.399923
l= 1 rc= 1.278952 Ekb= -1.755033
PSML: Total number of Kleinman-Bylander projectors: 8
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: nodes
NODES: Orbitals with angular momentum L= 0
NODES: Basis orbitals for state 2s
NODES: PAO cut-off radius determinated from an
NODES: energy shift= 0.010000 Ry
izeta = 1
lambda = 1.000000
rc = 4.511437
energy = -0.990536
kinetic = 0.937580
potential(screened) = -1.928116
potential(ionic) = -5.484011
izeta = 2
lambda = 1.000000
rc = 4.511437
energy = 0.891142
kinetic = 1.793173
potential(screened) = -0.902030
potential(ionic) = -3.534576
NODES: Orbitals with angular momentum L= 1
NODES: Basis orbitals for state 2p
NODES: PAO cut-off radius determinated from an
NODES: energy shift= 0.010000 Ry
izeta = 1
lambda = 1.000000
rc = 5.490449
energy = -0.370949
kinetic = 2.425333
potential(screened) = -2.796282
potential(ionic) = -6.202636
izeta = 2
lambda = 1.000000
rc = 5.490449
energy = 0.680157
kinetic = 2.141732
potential(screened) = -1.461575
potential(ionic) = -3.873772
*Note: V_local used for l= 2
** Using vlocal for PAOs with L= 2
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
*Note: V_local used for lpol= 2
** Using vlocal for PAOs with L= 2
Split based on tail norm
izeta = 1
rc = 5.490449
energy = 1.123484
kinetic = 2.219016
potential(screened) = -1.095531
potential(ionic) = -3.908003
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
2s( 2.00)
2p( 2.00)
3d( 0.00)
Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 5.490449
comcore: Pseudo-core radius Rcore= 1.671741
atom: _________________________________________________________________________
prinput: Basis input
PAO.BasisType nodes
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
# WARNING: This information might be incomplete!
C 2 # Species label, number of l-shells
n=2 0 2 # n, l, Nzeta
4.511 4.511
1.000 1.000
n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
5.490 5.490
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
Dumping basis to NetCDF file C.ion.nc
coor: Atomic-coordinates input format = Fractional
siesta: Atomic coordinates (Bohr) and species
siesta: 0.00000 0.00000 0.00000 1 1
siesta: 1.68516 1.68516 1.68516 1 2
siesta: System type = bulk
initatomlists: Number of atoms, orbitals, and projectors: 2 26 16
siesta: ******************** Simulation parameters ****************************
siesta:
siesta: The following are some of the parameters of the simulation.
siesta: A complete list of the parameters used, including default values,
siesta: can be found in file out.fdf
siesta:
redata: Spin configuration = none
redata: Number of spin components = 1
redata: Time-Reversal Symmetry = T
redata: Spin spiral = F
redata: Long output = F
redata: Number of Atomic Species = 1
redata: Charge density info will appear in .RHO file
redata: Write Mulliken charges (when) = none
redata: Write Mulliken Pop. = NO
redata: Write Hirshfeld charges (when) = none
redata: Write Voronoi charges (when) = none
redata: Write spin charge (when) = none
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 320.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 300
redata: SCF convergence failure will abort job
redata: SCF mix quantity = Hamiltonian
redata: Mix DM or H after convergence = F
redata: Recompute H after scf cycle = F
redata: Mix DM in first SCF step = T
redata: Write Pulay info on disk = F
redata: New DM Occupancy tolerance = 0.000000000001
redata: No kicks to SCF
redata: DM Mixing Weight for Kicks = 0.5000
redata: Require Harris convergence for SCF = F
redata: Harris energy tolerance for SCF = 0.000100 eV
redata: Require DM convergence for SCF = T
redata: DM tolerance for SCF = 0.000001
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = F
redata: Hamiltonian tolerance for SCF = 0.001000 eV
redata: Require (free) Energy convergence for SCF = F
redata: (free) Energy tolerance for SCF = 0.000100 eV
redata: Using DFT-D3 dispersion = F
redata: Using Saved Data (generic) = F
redata: Use continuation files for DM = F
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Diagonalization
redata: Electronic Temperature = 0.0000 K
redata: Fix the spin of the system = F
redata: Max. number of TDED Iter = 1
redata: Number of TDED substeps = 3
redata: Dynamics option = Single-point calculation
mix.SCF: Pulay mixing = Pulay
mix.SCF: Variant = stable
mix.SCF: History steps = 2
mix.SCF: Linear mixing weight = 0.250000
mix.SCF: Mixing weight = 0.250000
mix.SCF: SVD condition = 0.1000E-07
redata: Save all siesta data in one NC = F
redata: ***********************************************************************
%block SCF.Mixers
Pulay
%endblock SCF.Mixers
%block SCF.Mixer.Pulay
# Mixing method
method pulay
variant stable
# Mixing options
weight 0.2500
weight.linear 0.2500
history 2
%endblock SCF.Mixer.Pulay
DM_history_depth set to one: no extrapolation allowed by default for geometry relaxation
Size of DM history Fstack: 1
Total number of electrons: 8.000000
Total ionic charge: 8.000000
k-point displ. along 1 input, could be: 0.00 0.50
k-point displ. along 2 input, could be: 0.00 0.50
k-point displ. along 3 input, could be: 0.00 0.50
Kpoints in: 48 . Kpoints trimmed: 44
siesta: k-grid: Number of k-points = 44
siesta: k-points from Monkhorst-Pack grid
siesta: k-cutoff (effective) = 5.044 Ang
siesta: k-point supercell and displacements
siesta: k-grid: 4 0 0 0.000
siesta: k-grid: 0 4 0 0.000
siesta: k-grid: 0 0 4 0.000
diag: Algorithm = D&C
diag: Used triangular part = Lower
diag: Absolute tolerance = 0.100E-15
diag: Orthogonalization factor = 0.100E-05
diag: Memory factor = 1.0000
superc: Internal auxiliary supercell: 5 x 5 x 5 = 125
superc: Number of atoms, orbitals, and projectors: 250 3250 2000
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save TSHS files in MD/FC simulation = F
ts: Save DM and EDM matrices = F
ts: Only save the overlap matrix S = F
ts: **************************************************************
************************ Begin: TS CHECKS AND WARNINGS ************************
************************ End: TS CHECKS AND WARNINGS **************************
====================================
Single-point calculation
====================================
superc: Internal auxiliary supercell: 5 x 5 x 5 = 125
superc: Number of atoms, orbitals, and projectors: 250 3250 2000
outcell: Unit cell vectors (Ang):
0.000000 1.783500 1.783500
1.783500 0.000000 1.783500
1.783500 1.783500 0.000000
outcell: Cell vector modules (Ang) : 2.522250 2.522250 2.522250
outcell: Cell angles (23,13,12) (deg): 60.0000 60.0000 60.0000
outcell: Cell volume (Ang**3) : 11.3462
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=26 nrows=26 sparsity=81.5059 nnzs=55098, refcount: 7>
<dData1D:(new from dSpData1D) n=55098, refcount: 1>
refcount: 1>
new_DM -- step: 1
Initializing Density Matrix...
DM filled with atomic data:
<dSpData2D:DM initialized from atoms
<sparsity:sparsity for geom step 0
nrows_g=26 nrows=26 sparsity=81.5059 nnzs=55098, refcount: 8>
<dData2D:DM n=55098 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 44 443
InitMesh: MESH = 24 x 24 x 24 = 13824
InitMesh: Mesh cutoff (required, used) = 320.000 375.353 Ry
New grid distribution [1]: sub = 2
stepf: Methfessel-Paxton step function
Using Hermite-Gauss polynomials of order 1
siesta: Program's energy decomposition (eV):
siesta: Ebs = -118.490002
siesta: Eions = 564.323437
siesta: Ena = 150.085033
siesta: Ekin = 228.339916
siesta: Enl = -12.247917
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -11.496284
siesta: DUscf = 0.915093
siesta: DUext = 0.000000
siesta: Ex = -103.415496
siesta: Ec = -14.014502
siesta: Exc = -117.429998
siesta: EbV = 0.000000
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -318.683167
siesta: Etot = -326.157594
siesta: FreeEng = -326.157594
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -318.683167 -326.157594 -326.157594 1.067224 -5.701236 0.917221
timer: Routine,Calls,Time,% = IterSCF 1 0.826 26.90
scf: 2 -326.241349 -326.200147 -326.200147 0.007243 -5.504752 0.639878
scf: 3 -326.274979 -326.241237 -326.241237 0.015976 -5.059574 0.007629
scf: 4 -326.241244 -326.241241 -326.241241 0.000249 -5.061884 0.004773
scf: 5 -326.241245 -326.241243 -326.241243 0.000331 -5.063406 0.002070
scf: 6 -326.241245 -326.241244 -326.241244 0.000258 -5.063941 0.001454
scf: 7 -326.241245 -326.241244 -326.241244 0.000176 -5.063965 0.001111
scf: 8 -326.241244 -326.241244 -326.241244 0.000065 -5.063756 0.000786
scf: 9 -326.241244 -326.241244 -326.241244 0.000015 -5.063525 0.000502
scf: 10 -326.241244 -326.241244 -326.241244 0.000013 -5.063369 0.000341
scf: 11 -326.241244 -326.241244 -326.241244 0.000018 -5.063259 0.000175
scf: 12 -326.241244 -326.241244 -326.241244 0.000016 -5.063210 0.000077
scf: 13 -326.241244 -326.241244 -326.241244 0.000013 -5.063195 0.000071
scf: 14 -326.241244 -326.241244 -326.241244 0.000006 -5.063202 0.000051
scf: 15 -326.241244 -326.241244 -326.241244 0.000002 -5.063215 0.000034
scf: 16 -326.241244 -326.241244 -326.241244 0.000001 -5.063225 0.000023
SCF Convergence by DM criterion
max |DM_out - DM_in| : 0.0000006460
max |H_out - H_in| (eV) : 0.0000233713
SCF cycle converged after 16 iterations
Using DM_out to compute the final energy and forces
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 44 443
siesta: E_KS(eV) = -326.2412
siesta: E_KS - E_eggbox = -326.2412
siesta: Atomic forces (eV/Ang):
----------------------------------------
Tot -0.000000 -0.000000 0.000000
----------------------------------------
Max 0.000000
Res 0.000000 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.000000 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): -22.29 -22.29 -22.29 0.00 0.00 0.00
(Free)E + p*V (eV/cell) -326.0834
Target enthalpy (eV/cell) -326.2412
siesta: Program's energy decomposition (eV):
siesta: Ebs = -119.981824
siesta: Eions = 564.323437
siesta: Ena = 150.085033
siesta: Ekin = 224.616581
siesta: Enl = -11.704458
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -8.761412
siesta: DUscf = 0.666251
siesta: DUext = 0.000000
siesta: Ex = -102.832390
siesta: Ec = -13.987413
siesta: Exc = -116.819803
siesta: EbV = 0.000000
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -326.241244
siesta: Etot = -326.241244
siesta: FreeEng = -326.241244
siesta: Final energy (eV):
siesta: Band Struct. = -119.981824
siesta: Kinetic = 224.616581
siesta: Hartree = 24.953322
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch. = -102.832390
siesta: Corr. = -13.987413
siesta: Bulk bias = 0.000000
siesta: Exch.-corr. = -116.819803
siesta: Ion-electron = -265.230318
siesta: Ion-ion = -193.761027
siesta: Ekinion = 0.000000
siesta: D3 dispersion = 0.000000
siesta: Total = -326.241244
siesta: Fermi = -5.063225
siesta: Stress tensor (static) (eV/Ang**3):
siesta: -0.013911 0.000000 0.000000
siesta: 0.000000 -0.013911 0.000000
siesta: 0.000000 0.000000 -0.013911
siesta: Cell volume = 11.346171 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: 0.00015151 0.00015151 Ry/Bohr**3
siesta: 0.01391066 0.01391066 eV/Ang**3
siesta: 22.28733056 22.28733063 kBar
Basis Enthalpy Calculation:
Basis Pressure for species 1(C) : 0.2000000 GPa
Orbital volume contribution = 1.054049 eV
(Free)E + p_basis*V_orbitals = -325.187196 eV
(Free)Eharris+ p_basis*V_orbitals = -325.187196 eV
WARNING: BASIS_ENTHALPY and BASIS_HARRIS_ENTHALPY files are deprecated. They will be removed in future releases.
Please use system_label.BASIS_ENTHALPY in your scripts instead.
cite: Please indicate the Siesta version in published work: 5.4.2
cite: This calculation has made use of features in the following articles
cite: which we encourage you to cite in published work.
cite: (Please see "siesta.bib" for a BibTeX file.)
Primary SIESTA paper
DOI: www.doi.org/10.1088/0953-8984/14/11/302
PSML pseudopotential format
DOI: www.doi.org/10.1016/j.cpc.2018.02.011
timer: Elapsed wall time (sec) = 12.367
timer: CPU execution times (sec):
Routine Calls Time/call Tot.time %
siesta 1 16.561 16.561 100.00
Setup 1 1.150 1.150 6.94
bands 1 0.000 0.000 0.00
KSV_init 1 0.000 0.000 0.00
IterGeom 1 15.399 15.399 92.98
geom_init 1 1.096 1.096 6.62
state_init 1 0.209 0.209 1.26
hsparse 1 0.010 0.010 0.06
overlap 1 0.011 0.011 0.07
Setup_H0 1 0.412 0.412 2.49
naefs 2 0.000 0.000 0.00
dnaefs 1 0.000 0.000 0.00
two-body 1 0.000 0.000 0.00
MolMec 2 0.000 0.000 0.00
kinefsm 2 0.011 0.023 0.14
nlefsm 2 0.063 0.127 0.76
DHSCF_Init 1 0.356 0.356 2.15
DHSCF1 1 0.015 0.015 0.09
InitMesh 1 0.015 0.015 0.09
INITMESH 1 0.000 0.000 0.00
DHSCF2 1 0.341 0.341 2.06
REMESH 1 0.048 0.048 0.29
REORD 51 0.000 0.001 0.01
PHION 1 0.265 0.265 1.60
COMM_BSC 75 0.000 0.001 0.01
POISON 19 0.000 0.006 0.04
fft 38 0.000 0.004 0.02
setup_H 17 0.512 8.699 52.52
DHSCF 18 0.568 10.232 61.78
DHSCF3 18 0.508 9.150 55.25
rhoofd 18 0.321 5.770 34.84
XC 18 0.002 0.033 0.20
GXC-CellXC 18 0.002 0.032 0.20
gridxc@cellXC 18 0.002 0.032 0.19
vmat 18 0.185 3.337 20.15
IterSCF 16 0.791 12.655 76.42
compute_dm 16 0.276 4.410 26.63
diagon 16 0.276 4.408 26.62
c-eigval 704 0.002 1.508 9.10
c-buildHS 704 0.002 1.414 8.54
cdiag 1408 0.000 0.241 1.45
cdiag1 1408 0.000 0.011 0.07
cdiag2 1408 0.000 0.048 0.29
cdiag3 1408 0.000 0.155 0.94
c-eigvec 704 0.002 1.581 9.55
cdiag4 704 0.000 0.004 0.02
c-buildD 704 0.002 1.305 7.88
MIXER 15 0.000 0.004 0.03
PostSCF 1 1.648 1.648 9.95
FINAL_HF 1 1.648 1.648 9.95
DHSCF4 1 1.082 1.082 6.53
dfscf 1 1.053 1.053 6.36
overfsm 1 0.012 0.012 0.07
writeHSX 1 0.001 0.001 0.01
state_analysis 1 0.000 0.000 0.00
siesta_move 1 0.000 0.000 0.00
Analysis 1 0.001 0.001 0.01
optical 1 0.000 0.000 0.00
>> End of run: 31-JAN-2026 22:37:53
Job completed
Job completed
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