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Siesta_error
Raw
BASIS_ENTHALPY
-698.59609910092774
The above number is the electronic (free)energy: -701.17033831475794
Plus the pressure : 1.3595453680289311E-005 ( 0.20000000000000001 GPa)
times the orbital volume (in Bohr**3): 13916.534943485049
Raw
cbt.py
from __future__ import print_function, division
import os
import numpy as np
from sisl import *
import matplotlib.pyplot as plt
cbt = Geometry([[4.20500000000000, 2.25000000000000, 0.00000000000000 ], [2.62500000000000, 0.67000000000000 , 0.00000000000000], [1.04500000000000 , 2.25000000000000, 0.00000000000000],[2.62500000000000, 3.83000000000000 , 0.00000000000000]],
[Atom('Si'), Atom('Si'), Atom('Si'), Atom('Si')],
sc=SuperCell([5,5,30], origo=[-5] * 3))
#open('RUN.fdf', 'w').write("""%include STRUCT.fdf
#SystemLabel siesta_2
#PAO.BasisSize SZP
#MeshCutoff 250. Ry
#CDF.Save true
#CDF.Compress 9
#SaveHS true
#SaveRho true
#%block kgrid.MonkhorstPack
# 61 1 1 0.
# 1 61 1 0.
# 0 0 1 0.
#%endblock
#""")
#cbt.write('STRUCT.fdf')
fdf = get_sile('RUN.fdf')
H = fdf.read_hamiltonian()
print(H)
Raw
dump
netcdf siesta_2 {
dimensions:
n_s = 25 ;
na_u = 4 ;
spin = 1 ;
one = 1 ;
no_u = 52 ;
no_s = 1300 ;
xyz = 3 ;
variables:
int lasto(na_u) ;
lasto:info = "Last orbital of equivalent atom" ;
double Qtot(one) ;
Qtot:info = "Total charge" ;
int nsc(xyz) ;
nsc:info = "Number of supercells in each unit-cell direction" ;
double Ef(one) ;
Ef:unit = "Ry" ;
Ef:info = "Fermi level" ;
double xa(na_u, xyz) ;
xa:unit = "Bohr" ;
xa:info = "Atomic coordinates" ;
double cell(xyz, xyz) ;
cell:unit = "Bohr" ;
cell:info = "Unit cell" ;
double fa(na_u, xyz) ;
fa:unit = "Ry/Bohr" ;
fa:info = "Atomic forces" ;
double stress(xyz, xyz) ;
stress:unit = "Ry/Bohr**3" ;
stress:info = "Cell stress" ;
// global attributes:
:method = "diagon" ;
:name = "" ;
:time = "2020-02-14T15-51-44" ;
:label = "siesta_2" ;
group: SPARSE {
dimensions:
nnzs = 18124 ;
spin_EDM = 1 ;
variables:
int isc_off(n_s, xyz) ;
isc_off:info = "Index of supercell coordinates" ;
int n_col(no_u) ;
n_col:info = "Number of non-zero elements per row" ;
int list_col(nnzs) ;
list_col:info = "Supercell column indices in the sparse format" ;
double S(nnzs) ;
S:info = "Overlap matrix" ;
double DM(spin, nnzs) ;
DM:info = "Density matrix" ;
double EDM(spin_EDM, nnzs) ;
EDM:unit = "Ry" ;
EDM:info = "Energy density matrix" ;
double H(spin, nnzs) ;
H:unit = "Ry" ;
H:info = "Hamiltonian" ;
} // group SPARSE
group: GRID {
dimensions:
spin = 1 ;
nx = 48 ;
ny = 48 ;
nz = 288 ;
variables:
double Rho(spin, nz, ny, nx) ;
Rho:unit = "e/Bohr**3" ;
Rho:info = "Charge density" ;
} // group GRID
group: SETTINGS {
variables:
double DMTolerance(one) ;
DMTolerance:info = "Tolerance for converging the density matrix" ;
double HTolerance(one) ;
HTolerance:info = "Tolerance for converging the Hamiltonian" ;
double NetCharge(one) ;
NetCharge:info = "Net charge of the system" ;
double MixingWeight(one) ;
MixingWeight:info = "Mixing weight" ;
int BZ(xyz, xyz) ;
BZ:info = "Grid used for the Brillouin zone integration" ;
double BZ_displ(xyz) ;
BZ_displ:unit = "b**-1" ;
BZ_displ:info = "Grid displacement used in Brillouin zone" ;
double ElectronicTemperature(one) ;
ElectronicTemperature:unit = "Ry" ;
ElectronicTemperature:info = "Temperature for electrons" ;
double MeshCutoff(one) ;
MeshCutoff:unit = "Ry" ;
MeshCutoff:info = "Mesh cutoff for real space grid" ;
} // group SETTINGS
group: BASIS {
variables:
int basis(na_u) ;
basis:info = "Basis of each atom by ID" ;
group: Si {
dimensions:
norbs = 5 ;
nkbs = 4 ;
ntb = 500 ;
variables:
int orbnl_ispol(norbs) ;
int orbnl_z(norbs) ;
int orbnl_n(norbs) ;
int orbnl_l(norbs) ;
double cutoff(norbs) ;
double delta(norbs) ;
double orbnl_pop(norbs) ;
double kbcutoff(nkbs) ;
double pjnl_ekb(nkbs) ;
int pjnl_l(nkbs) ;
int pjnl_n(nkbs) ;
double pjnl_j(nkbs) ;
double kbdelta(nkbs) ;
double orb(norbs, ntb) ;
double vna(ntb) ;
vna:cutoff = 6.27086583269337 ;
vna:delta = 0.0125668653961791 ;
double chlocal(ntb) ;
chlocal:cutoff = 2.4864884811 ;
chlocal:delta = 0.00498294284789579 ;
double reduced_vlocal(ntb) ;
reduced_vlocal:cutoff = 2.16703737683 ;
reduced_vlocal:delta = 0.00434276027420842 ;
double core(ntb) ;
core:cutoff = 2.99931413458 ;
core:delta = 0.00601064956829659 ;
double proj(nkbs, ntb) ;
// group attributes:
:ID = 1 ;
:Atomic_number = 14 ;
:Mass = 28.09 ;
:Element = "Si" ;
:Self_energy = 13.7044238193695 ;
:Number_of_projectors = 16 ;
:Valence_charge = 4. ;
:Number_of_orbitals = 13 ;
:L_max_basis = 2 ;
:L_max_projs = 3 ;
:Label = "Si" ;
} // group Si
} // group BASIS
}
Raw
filelist
RUN.fdf
CLOCK
BASIS_ENTHALPY
PARALLEL_DIST
RUN.out
cbt.py
siesta_2.STRUCT_OUT
STRUCT.fdf
OCCS
Si.ion
siesta_2.nc
siesta_2.KP
MESSAGES
siesta_2.FA
siesta_2.ORB_INDX
Si.psf
BASIS_HARRIS_ENTHALPY
NON_TRIMMED_KP_LIST
Si.ion.nc
siesta_2.RHO
siesta_2.EIG
Si.zip
filelits.txt
siesta_2.BONDS
OUTVARS.yml
Si.ion.xml
fdf-05580.log
RUNnew.out
siesta_2.bib
fdf-90769.log
siesta_2.BONDS_FINAL
fdf-16111.log
FORCE_STRESS
siesta_2.DM
RUN2.out
siesta_2.XV
siesta_2.HSX
Raw
RUN.fdf
%include STRUCT.fdf
SystemLabel siesta_2
PAO.BasisSize DZP
MeshCutoff 250. Ry
CDF.Save true
CDF.Compress 9
SaveHS true
SaveRho true
%block kgrid.MonkhorstPack
61 1 1 0.
1 61 1 0.
0 0 1 0.
%endblock
Raw
RUN.out
Siesta Version : v4.1-b4
Architecture : unknown
Compiler version: GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Compiler flags : f77 -O2 -fPIC -ftree-vectorize -march=native
PP flags : -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4
Libraries : /usr/lib/libblas.so /usr/lib/liblapack.so libncdf.a libfdict.a -L/lib -lnetcddff -lnetcdf /usr/lib/libblas.so /usr/lib/liblapack.so libncdf.a libfdict.a
SERIAL version
NetCDF support
NetCDF-4 support
* Running in serial mode
>> Start of run: 14-FEB-2020 15:36:59
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from RUN.fdf
reinit: -----------------------------------------------------------------------
reinit: System Name:
reinit: -----------------------------------------------------------------------
reinit: System Label: siesta_2
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 14 Label: Si
Ground state valence configuration: 3s02 3p02
Reading pseudopotential information in formatted form from Si.psf
Pseudopotential generated from a relativistic atomic calculation
Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.47
3p( 2.00) rc: 2.14
3d( 0.00) rc: 1.43
4f( 0.00) rc: 1.49
For Si, 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.
<basis_specs>
===============================================================================
Si Z= 14 Mass= 28.090 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=3
n=1 nzeta=2 polorb=0
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
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=3
n=1 nzeta=2 polorb=1
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 0.0000 0.0000
lambdas: 1.0000 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=1 erefs: 0.17977+309
L=3 Nkbl=1 erefs: 0.17977+309
===============================================================================
</basis_specs>
atom: Called for Si (Z = 14)
read_vps: Pseudopotential generation method:
read_vps: ATM3.3.2 Troullier-Martins
Total valence charge: 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
V l=0 = -2*Zval/r beyond r= 2.1135
V l=1 = -2*Zval/r beyond r= 2.1943
V l=2 = -2*Zval/r beyond r= 2.1135
V l=3 = -2*Zval/r beyond r= 2.1135
All V_l potentials equal beyond r= 2.0873
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 2.1943
VLOCAL1: 99.0% of the norm of Vloc inside 9.963 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 22.707 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.48649
atom: Maximum radius for r*vlocal+2*Zval: 2.16704
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
GHOST: No ghost state for L = 3
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 2.335829 el= -0.802399 Ekb= 5.684867 kbcos= 0.289142
l= 1 rc= 2.486488 el= -0.306542 Ekb= 2.151057 kbcos= 0.277002
l= 2 rc= 2.455599 el= 0.002313 Ekb= -3.900592 kbcos= -0.042122
l= 3 rc= 2.680160 el= 0.003402 Ekb= -1.094260 kbcos= -0.004535
KBgen: Total number of Kleinman-Bylander projectors: 16
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 3s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 5.007352
energy = -0.783862
kinetic = 0.580827
potential(screened) = -1.364689
potential(ionic) = -3.762135
izeta = 2
rmatch = 4.418952
splitnorm = 0.150000
energy = -0.687272
kinetic = 0.886021
potential(screened) = -1.573293
potential(ionic) = -4.067038
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 3p
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 6.270866
energy = -0.288429
kinetic = 0.877136
potential(screened) = -1.165564
potential(ionic) = -3.385227
izeta = 2
rmatch = 5.007352
splitnorm = 0.150000
energy = -0.193575
kinetic = 1.272408
potential(screened) = -1.465983
potential(ionic) = -3.856098
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 3p
izeta = 1
rc = 6.270866
energy = 0.431823
kinetic = 1.297894
potential(screened) = -0.866071
potential(ionic) = -2.920426
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
3s( 2.00)
3p( 2.00)
Vna: chval, zval: 4.00000 4.00000
Vna: Cut-off radius for the neutral-atom potential: 6.270866
comcore: Pseudo-core radius Rcore= 2.999314
atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 14 Si # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
Si 2 # Species label, number of l-shells
n=3 0 2 # n, l, Nzeta
5.007 4.419
1.000 1.000
n=3 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
6.271 5.007
1.000 1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: Atomic coordinates (Bohr) and species
siesta: 7.94630 4.25189 0.00000 1 1
siesta: 4.96053 1.26612 0.00000 1 2
siesta: 1.97476 4.25189 0.00000 1 3
siesta: 4.96053 7.23765 0.00000 1 4
siesta: System type = slab
initatomlists: Number of atoms, orbitals, and projectors: 4 52 64
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 Pop. = NO
redata: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 250.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 1000
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 Mixing Weight = 0.2500
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 = 0.000100
redata: Require EDM convergence for SCF = F
redata: EDM tolerance for SCF = 0.001000 eV
redata: Require H convergence for SCF = T
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 Saved Data (generic) = F
redata: Use continuation files for DM = F
redata: Neglect nonoverlap interactions = F
redata: Method of Calculation = Diagonalization
redata: Electronic Temperature = 299.9869 K
redata: Fix the spin of the system = F
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: ***********************************************************************
%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: 16.000000
Total ionic charge: 16.000000
k-point displ. along 1 input, could be: 0.00 0.50
Kpoints in: 1861 . Kpoints trimmed: 1861
siesta: k-grid: Number of k-points = 1861
siesta: k-grid: Cutoff (effective) = 15.000 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 61 1 1 0.000
siesta: k-grid: 1 61 1 0.000
siesta: k-grid: 0 0 1 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 1 = 25
superc: Number of atoms, orbitals, and projectors: 100 1300 1600
ts: **************************************************************
ts: Save H and S matrices = F
ts: Save DM and EDM matrices = F
ts: Fix Hartree potential = 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 1 = 25
superc: Number of atoms, orbitals, and projectors: 100 1300 1600
outcell: Unit cell vectors (Ang):
5.000000 0.000000 0.000000
0.000000 5.000000 0.000000
0.000000 0.000000 30.000000
outcell: Cell vector modules (Ang) : 5.000000 5.000000 30.000000
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 750.0000
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=52 nrows=52 sparsity=6.7027 nnzs=18124, refcount: 7>
<dData1D:(new from dSpData1D) n=18124, 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=52 nrows=52 sparsity=6.7027 nnzs=18124, refcount: 8>
<dData2D:DM n=18124 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 16 113
New grid distribution: 1
1 1: 24 1: 24 1: 144
InitMesh: MESH = 48 x 48 x 288 = 663552
InitMesh: (bp) = 24 x 24 x 144 = 82944
InitMesh: Mesh cutoff (required, used) = 250.000 254.709 Ry
ExtMesh (bp) on 0 = 88 x 88 x 208 = 1610752
PhiOnMesh: Number of (b)points on node 0 = 82944
PhiOnMesh: nlist on node 0 = 757320
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -151.252841
siesta: Eions = 745.838598
siesta: Ena = 213.902710
siesta: Ekin = 174.311245
siesta: Enl = 77.281391
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 2.843479
siesta: DUscf = 0.656220
siesta: DUext = 0.000000
siesta: Enegf = 0.000000
siesta: Exc = -424.264443
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -695.856007
siesta: Etot = -701.107996
siesta: FreeEng = -701.109760
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -695.856007 -701.107996 -701.109760 1.855284 -4.652641 0.625546
timer: Routine,Calls,Time,% = IterSCF 1 34.156 93.71
scf: 2 -701.185568 -701.150574 -701.152390 0.008816 -4.551849 0.430401
scf: 3 -701.176440 -701.167098 -701.168925 0.012026 -4.409762 0.102721
scf: 4 -701.169071 -701.168157 -701.169983 0.001615 -4.389032 0.032720
scf: 5 -701.168701 -701.168471 -701.170297 0.001009 -4.381260 0.009219
scf: 6 -701.168513 -701.168493 -701.170319 0.000241 -4.382770 0.006739
scf: 7 -701.168521 -701.168508 -701.170334 0.000370 -4.384909 0.002723
scf: 8 -701.168513 -701.168511 -701.170337 0.000149 -4.385573 0.001133
scf: 9 -701.168513 -701.168512 -701.170338 0.000108 -4.385900 0.000373
scf: 10 -701.168512 -701.168512 -701.170338 0.000017 -4.385852 0.000323
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000171688
max |H_out - H_in| (eV) : 0.0003231947
SCF cycle converged after 10 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: 16 113
siesta: E_KS(eV) = -701.1685
siesta: E_KS - E_eggbox = -701.1685
siesta: Atomic forces (eV/Ang):
----------------------------------------
Tot -0.012572 0.003538 0.000000
----------------------------------------
Max 10.092863
Res 5.822348 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 10.092863 constrained
Stress-tensor-Voigt (kbar): -52.00 -52.04 0.00 -0.01 0.00 -0.00
(Free)E + p*V (eV/cell) -684.9364
Target enthalpy (eV/cell) -701.1703
siesta: Program's energy decomposition (eV):
siesta: Ebs = -153.591458
siesta: Eions = 745.838598
siesta: Ena = 213.902710
siesta: Ekin = 172.857340
siesta: Enl = 76.978616
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = 4.208202
siesta: DUscf = 0.504133
siesta: DUext = 0.000000
siesta: Enegf = 0.000000
siesta: Exc = -423.780915
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -701.168512
siesta: Etot = -701.168512
siesta: FreeEng = -701.170338
siesta: Final energy (eV):
siesta: Band Struct. = -153.591458
siesta: Kinetic = 172.857340
siesta: Hartree = 1975.175745
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Enegf = 0.000000
siesta: Exch.-corr. = -423.780915
siesta: Ion-electron = -4091.952376
siesta: Ion-ion = 1666.531694
siesta: Ekinion = 0.000000
siesta: Total = -701.168512
siesta: Fermi = -4.385852
siesta: Atomic forces (eV/Ang):
siesta: 1 -10.092863 -0.001334 -0.000000
siesta: 2 -0.000645 10.082803 0.000000
siesta: 3 10.083183 0.001623 -0.000000
siesta: 4 -0.002247 -10.079554 0.000000
siesta: ----------------------------------------
siesta: Tot -0.012572 0.003538 0.000000
siesta: Stress tensor (static) (eV/Ang**3):
siesta: -0.032455 -0.000009 0.000000
siesta: -0.000009 -0.032482 -0.000000
siesta: -0.000000 0.000000 0.000002
siesta: Cell volume = 750.000000 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: 0.00023574 0.00054426 Ry/Bohr**3
siesta: 0.02164519 0.04997171 eV/Ang**3
siesta: 34.67979461 80.06437839 kBar
(Free)E+ p_basis*V_orbitals = -698.596099
(Free)Eharris+ p_basis*V_orbitals = -698.596099
siesta: Electric dipole (a.u.) = -0.000000 -0.000000 -0.000000
siesta: Electric dipole (Debye) = -0.000000 -0.000000 -0.000000
timer: Elapsed wall time (sec) = 198.648
timer: CPU execution times (sec):
Routine Calls Time/call Tot.time %
siesta 1 366.344 366.344 100.00
Setup 1 0.340 0.340 0.09
bands 1 0.000 0.000 0.00
KSV_init 1 0.000 0.000 0.00
IterGeom 1 365.532 365.532 99.78
state_init 1 0.160 0.160 0.04
hsparse 1 0.004 0.004 0.00
overlap 1 0.152 0.152 0.04
Setup_H0 1 1.792 1.792 0.49
naefs 2 0.000 0.000 0.00
MolMec 2 0.000 0.000 0.00
kinefsm 2 0.074 0.148 0.04
nlefsm 2 0.332 0.664 0.18
DHSCF_Init 1 1.028 1.028 0.28
DHSCF1 1 0.052 0.052 0.01
INITMESH 1 0.000 0.000 0.00
DHSCF2 1 0.976 0.976 0.27
REMESH 1 0.072 0.072 0.02
REORD 40 0.002 0.092 0.03
PHION 1 0.732 0.732 0.20
COMM_BSC 28 0.003 0.072 0.02
POISON 14 0.076 1.068 0.29
fft 28 0.029 0.816 0.22
IterSCF 10 36.169 361.692 98.73
setup_H 11 0.632 6.952 1.90
DHSCF 13 0.702 9.128 2.49
DHSCF3 13 0.600 7.796 2.13
rhoofd 13 0.308 4.000 1.09
CellXC 13 0.040 0.516 0.14
cellXC 13 0.040 0.516 0.14
vmat 12 0.158 1.900 0.52
writeHSX 12 0.002 0.028 0.01
compute_dm 10 35.473 354.728 96.83
diagon 10 35.473 354.728 96.83
c-eigval 18610 0.006 118.644 32.39
c-buildHS 18610 0.002 32.217 8.79
cdiag 37220 0.007 243.691 66.52
cdiag1 37220 0.003 102.639 28.02
cdiag2 37220 0.001 46.597 12.72
cdiag3 37220 0.002 73.852 20.16
c-eigvec 18610 0.010 192.268 52.48
cdiag4 18610 0.001 18.535 5.06
c-buildD 18610 0.002 42.144 11.50
MIXER 9 0.000 0.004 0.00
PostSCF 1 1.888 1.888 0.52
DHSCF4 1 1.332 1.332 0.36
dfscf 1 1.236 1.236 0.34
overfsm 1 0.008 0.008 0.00
state_analysis 1 0.000 0.000 0.00
siesta_move 1 0.000 0.000 0.00
Analysis 1 0.472 0.472 0.13
siesta_analysis 1 0.472 0.472 0.13
optical 1 0.000 0.000 0.00
>> End of run: 14-FEB-2020 15:40:17
Job completed
Raw
Struct.fdf
LatticeConstant 1.0 Ang
%block LatticeVectors
5.00000000 0.00000000 0.00000000
0.00000000 5.00000000 0.00000000
0.00000000 0.00000000 30.00000000
%endblock LatticeVectors
NumberOfAtoms 4
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
4.20500000 2.25000000 0.00000000 1 # 1: Si
2.62500000 0.67000000 0.00000000 1 # 2: Si
1.04500000 2.25000000 0.00000000 1 # 3: Si
2.62500000 3.83000000 0.00000000 1 # 4: Si
%endblock AtomicCoordinatesAndAtomicSpecies
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 14 Si
%endblock ChemicalSpeciesLabel
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