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************************************************附上4.1.b3结果
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumped input in INPUT_TMP.47960
************************** Dump of input data file ****************************
SystemName Water molecule
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
MeshCutoff 50 Ry
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H
%endblock ChemicalSpeciesLabel
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
0.000 0.000 0.000 1
0.757 0.586 0.000 2
-0.757 0.586 0.000 2
%endblock AtomicCoordinatesAndAtomicSpecies
save-rho T
save-delta-rho T
save-total-potential T
save-neutral-atom-potential T
save-hs T
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
Siesta Version: siesta-4.1--736
Architecture : unknown
Compiler flags: mpiifort -O2 -fPIC
PP flags : -DFC_HAVE_ABORT -DMPI
Libraries : -L/opt/intel/mkl/lib/intel64 -I/opt/intel/mkl/include/lib -lmkl_blas95_lp64 -lmkl_lapack95_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_core -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_rt -liomp5 -lpthread -lm
PARALLEL version
* Running on 4 nodes in parallel
>> Start of run: 14-OCT-2017 4:13:42
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Atomic number: 8 Label: O
Species number: 2 Atomic number: 1 Label: H
Ground state valence configuration: 2s02 2p04
Reading pseudopotential information in formatted form from O.psf
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.14
2p( 4.00) rc: 1.14
3d( 0.00) rc: 1.14
4f( 0.00) rc: 1.14
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.25
2p( 0.00) rc: 1.25
3d( 0.00) rc: 1.25
4f( 0.00) rc: 1.25
For O, 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.
For H, standard SIESTA heuristics set lmxkb to 2
(one more than the basis l, including polarization orbitals).
Use PS.lmax or PS.KBprojectors blocks to override.
<basis_specs>
===============================================================================
O Z= 8 Mass= 16.000 Charge= 0.17977+309
Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=2
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=2
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 O (Z = 8)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.1278
V l=1 = -2*Zval/r beyond r= 1.1278
V l=2 = -2*Zval/r beyond r= 1.1278
V l=3 = -2*Zval/r beyond r= 1.1138
All V_l potentials equal beyond r= 1.1278
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.1278
VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759
atom: Maximum radius for r*vlocal+2*Zval: 1.18566
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= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= 0.326910
l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= -0.395047
l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= -0.003484
l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= -0.000344
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 2s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 3.305093
energy = -1.723766
kinetic = 1.614911
potential(screened) = -3.338677
potential(ionic) = -11.304675
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.471299
kinetic = 2.446434
potential(screened) = -3.917732
potential(ionic) = -12.476133
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 2p
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 3.937239
energy = -0.658841
kinetic = 5.005986
potential(screened) = -5.664827
potential(ionic) = -13.452360
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.367441
kinetic = 7.530509
potential(screened) = -7.897949
potential(ionic) = -16.611953
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.398520
kinetic = 4.716729
potential(screened) = -2.318209
potential(ionic) = -8.603170
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
2s( 2.00)
2p( 4.00)
Vna: chval, zval: 6.00000 6.00000
Vna: Cut-off radius for the neutral-atom potential: 3.937239
atom: _________________________________________________________________________
<basis_specs>
===============================================================================
H Z= 1 Mass= 1.0100 Charge= 0.17977+309
Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
L=0 Nsemic=0 Cnfigmx=1
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
===============================================================================
</basis_specs>
atom: Called for H (Z = 1)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2343
V l=1 = -2*Zval/r beyond r= 1.2189
V l=2 = -2*Zval/r beyond r= 1.2189
All V_l potentials equal beyond r= 1.2343
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2343
VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251
atom: Maximum radius for r*vlocal+2*Zval: 1.21892
GHOST: No ghost state for L = 0
GHOST: No ghost state for L = 1
GHOST: No ghost state for L = 2
KBgen: Kleinman-Bylander projectors:
l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= -0.336422
l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= -0.021697
l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= -0.002281
KBgen: Total number of Kleinman-Bylander projectors: 9
atom: -------------------------------------------------------------------------
atom: SANKEY-TYPE ORBITALS:
atom: Selected multiple-zeta basis: split
SPLIT: Orbitals with angular momentum L= 0
SPLIT: Basis orbitals for state 1s
SPLIT: PAO cut-off radius determined from an
SPLIT: energy shift= 0.020000 Ry
izeta = 1
lambda = 1.000000
rc = 4.828263
energy = -0.449375
kinetic = 0.929372
potential(screened) = -1.378747
potential(ionic) = -1.915047
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336153
kinetic = 1.505294
potential(screened) = -1.841447
potential(ionic) = -2.413582
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.706972
kinetic = 1.396397
potential(screened) = -0.689424
potential(ionic) = -1.169792
atom: Total number of Sankey-type orbitals: 5
atm_pop: Valence configuration (for local Pseudopot. screening):
1s( 1.00)
Vna: chval, zval: 1.00000 1.00000
Vna: Cut-off radius for the neutral-atom potential: 4.828263
atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 8 O # Species index, atomic number, species label
2 1 H # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
O 2 # Species label, number of l-shells
n=2 0 2 # n, l, Nzeta
3.305 2.510
1.000 1.000
n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
3.937 2.542
1.000 1.000
H 1 # Species label, number of l-shells
n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
4.828 3.855
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: 0.00000 0.00000 0.00000 1 1
siesta: 1.43052 1.10738 0.00000 2 2
siesta: -1.43052 1.10738 0.00000 2 3
siesta: Automatic unit cell vectors (Ang):
siesta: 7.286412 0.000000 0.000000
siesta: 0.000000 5.746952 0.000000
siesta: 0.000000 0.000000 5.621012
siesta: System type = molecule
initatomlists: Number of atoms, orbitals, and projectors: 3 23 34
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 = 2
redata: Charge density info will appear in .RHO file
redata: Write Mulliken Pop. = NO
redata: Mesh Cutoff = 50.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Min. number of SCF Iter = 0
redata: Max. number of SCF Iter = 50
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 = 0.0001
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: Divide and Conquer = T
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: 8.000000
Total ionic charge: 8.000000
* ProcessorY, Blocksize: 2 6
* Orbital distribution balance (max,min): 6 5
Kpoints in: 1 . Kpoints trimmed: 1
siesta: k-grid: Number of k-points = 1
siesta: k-grid: Cutoff (effective) = 2.811 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 1 0 0 0.000
siesta: k-grid: 0 1 0 0.000
siesta: k-grid: 0 0 1 0.000
====================================
Single-point calculation
====================================
outcell: Unit cell vectors (Ang):
7.286412 0.000000 0.000000
0.000000 5.746952 0.000000
0.000000 0.000000 5.621012
outcell: Cell vector modules (Ang) : 7.286412 5.746952 5.621012
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 235.3780
<dSpData1D:S at geom step 0
<sparsity:sparsity for geom step 0
nrows_g=23 nrows=6 sparsity=.2609 nnzs=138, refcount: 7>
<dData1D:(new from dSpData1D) n=138, 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=23 nrows=6 sparsity=.2609 nnzs=138, refcount: 8>
<dData2D:DM n=138 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
New grid distribution: 1
1 1: 16 1: 8 1: 6
2 1: 16 1: 8 7: 12
3 1: 16 9: 15 1: 6
4 1: 16 9: 15 7: 12
InitMesh: MESH = 32 x 30 x 24 = 23040
InitMesh: (bp) = 16 x 15 x 12 = 2880
InitMesh: Mesh cutoff (required, used) = 50.000 50.384 Ry
ExtMesh (bp) on 0 = 40 x 36 x 30 = 43200
New grid distribution: 2
1 5: 16 1: 4 1: 12
2 1: 4 1: 4 1: 12
3 5: 16 5: 15 1: 12
4 1: 4 5: 15 1: 12
New grid distribution: 3
1 8: 16 1: 5 1: 12
2 1: 7 1: 5 1: 12
3 8: 16 6: 15 1: 12
4 1: 7 6: 15 1: 12
Setting up quadratic distribution...
ExtMesh (bp) on 0 = 36 x 32 x 36 = 41472
PhiOnMesh: Number of (b)points on node 0 = 576
PhiOnMesh: nlist on node 0 = 3687
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -86.527724
siesta: Eions = 815.854478
siesta: Ena = 175.154321
siesta: Ekin = 370.751247
siesta: Enl = -67.181676
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = -13.606312
siesta: DUscf = 1.705533
siesta: DUext = 0.000000
siesta: Exc = -116.213094
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -467.645208
siesta: Etot = -465.244458
siesta: FreeEng = -465.244458
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -467.645208 -465.244458 -465.244458 1.438730 -4.254018 6.304092
timer: Routine,Calls,Time,% = IterSCF 1 0.028 3.09
scf: 2 -466.124875 -465.763870 -465.763870 0.046622 -3.203898 2.536085
scf: 3 -465.849696 -465.836459 -465.836459 0.025064 -2.450205 0.346690
scf: 4 -465.841502 -465.839128 -465.839128 0.010781 -2.371205 0.255425
scf: 5 -465.841092 -465.840518 -465.840518 0.023618 -2.152275 0.044619
scf: 6 -465.840727 -465.840635 -465.840635 0.001580 -2.149639 0.027740
scf: 7 -465.840689 -465.840665 -465.840665 0.000885 -2.149921 0.014627
scf: 8 -465.840677 -465.840671 -465.840671 0.000436 -2.152067 0.010016
scf: 9 -465.840674 -465.840673 -465.840673 0.000473 -2.156136 0.003322
scf: 10 -465.840673 -465.840673 -465.840673 0.000044 -2.157561 0.001940
scf: 11 -465.840673 -465.840673 -465.840673 0.000014 -2.158566 0.001317
scf: 12 -465.840673 -465.840673 -465.840673 0.000015 -2.158751 0.000747
SCF Convergence by DM+H criterion
max |DM_out - DM_in| : 0.0000151486
max |H_out - H_in| (eV) : 0.0007470259
SCF cycle converged after 12 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: 3 23
siesta: E_KS(eV) = -465.8407
siesta: E_KS - E_eggbox = -465.8407
siesta: Atomic forces (eV/Ang):
----------------------------------------
Tot 0.000000 0.055861 -0.000000
----------------------------------------
Max 0.717766
Res 0.399597 sqrt( Sum f_i^2 / 3N )
----------------------------------------
Max 0.717766 constrained
Stress-tensor-Voigt (kbar): -20.20 -3.68 22.43 0.00 0.00 -0.00
(Free)E + p*V (eV/cell) -465.7698
Target enthalpy (eV/cell) -465.8407
siesta: Program's energy decomposition (eV):
siesta: Ebs = -104.740961
siesta: Eions = 815.854478
siesta: Ena = 175.154321
siesta: Ekin = 350.790387
siesta: Enl = -61.961783
siesta: Eso = 0.000000
siesta: Eldau = 0.000000
siesta: DEna = -1.781929
siesta: DUscf = 0.727495
siesta: DUext = 0.000000
siesta: Exc = -112.914686
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -465.840673
siesta: Etot = -465.840673
siesta: FreeEng = -465.840673
siesta: Final energy (eV):
siesta: Band Struct. = -104.740961
siesta: Kinetic = 350.790387
siesta: Hartree = 382.623367
siesta: Eldau = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -112.914686
siesta: Ion-electron = -1072.833868
siesta: Ion-ion = -13.505875
siesta: Ekinion = 0.000000
siesta: Total = -465.840673
siesta: Fermi = -2.158751
siesta: Atomic forces (eV/Ang):
siesta: 1 0.000000 -0.501435 -0.000000
siesta: 2 0.717766 0.278648 -0.000000
siesta: 3 -0.717766 0.278648 -0.000000
siesta: ----------------------------------------
siesta: Tot 0.000000 0.055861 -0.000000
siesta: Stress tensor (static) (eV/Ang**3):
siesta: -0.012608 0.000000 -0.000000
siesta: 0.000000 -0.002294 -0.000000
siesta: -0.000000 0.000000 0.013999
siesta: Cell volume = 235.378012 Ang**3
siesta: Pressure (static):
siesta: Solid Molecule Units
siesta: 0.00000328 -0.00001818 Ry/Bohr**3
siesta: 0.00030112 -0.00166940 eV/Ang**3
siesta: 0.48244709 -2.67470419 kBar
(Free)E+ p_basis*V_orbitals = -465.255506
(Free)Eharris+ p_basis*V_orbitals = -465.255506
siesta: Electric dipole (a.u.) = -0.000000 0.558282 0.000000
siesta: Electric dipole (Debye) = -0.000000 1.419012 0.000000
dhscf: Vacuum level (max, mean) = 0.636974 -0.068254 eV
>> End of run: 14-OCT-2017 4:13:45
Job completed
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发表于 Post on 2016-7-22 00:18:13
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