Dear siesta users! I get the following error message while trying to do a structure relaxation:
atom: Including non-local core corrections could be a good idea
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.19072
atom: Maximum radius for r*vlocal+2*Zval: 1.98224
GHOST: WARNING: Ghost state for L = 0
GHOST: No ghost state for L = 1
KBgen: More than one KB projector for l= 2
KBgen: ghost states analysis will be not performed
KBgen: WARNING: Ghost states have been detected
KBgen: WARNING: Some parameter should be changed in the
KBgen: WARNING: pseudopotential generation procedure.
Stopping Program from Node: 0
I attach my .fdf file together with the input file for germanium
pseudopotential generation. Also, the whole output message is attached
below. I'd appreciate any thoughts on how to deal with this error.
Thank you!
Sincerely,
Gleb G.
GeH.fdf:
# test .fdf file for hydrogen-passivated germanium
# NW structure relaxation
SystemName Hexagonal passivated GeNW
SystemLabel GeH
## single-zeta basis plus
## polarization orbitals
Number_of_species 2
%block Ps.lmax
Ge 2
%endblock Ps.lmax
%block ChemicalSpeciesLabel
1 32 Ge
2 1 H
%endblock ChemicalSpeciesLabel
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 200 eV # 0.02 Ry by default
PAO.SplitNorm 0.15
## The block below is unclear. Pasted
## from passivated silicon.
%Block PAO.Basis
Ge 4 1.34026
n=3 2 2
6.0 5.0
1.0 1.0
n=4 0 2 E 18.70507 5.90867
7.12964 1.92417
1.00000 1.00000
n=4 1 2 E 81.00495 6.05123
7.71516 4.92203
1.00000 1.00000
n=4 2 1 E 29.55634 5.20733
7.78841
1.00000
%EndBlock PAO.Basis
#%block PAO.basis
#Ge 3 1.34026
#n=4 0 2 E 18.70507 5.90867
#7.12964 1.92417
#1.00000 1.00000
#n=4 1 2 E 81.00495 6.05123
#7.71516 4.92203
#1.00000 1.00000
#n=4 2 1 E 29.55634 5.20733
#7.78841
#1.00000
# H 1
# 0 2
# 5.00 0.00
#%endblock PAO.basis
# the following was inside PAO.Basis and didn't work
# Ge 4 split 0.0
# n=3 2 2 E 50.0 2.5
# 4.5 4.5
# n=4 0 2 P 2
# 5.0 5.0
# 1 2 P 2
# 5.0 5.0
#H 2 0.22
# n=1 0 2 E 2.07 0.00
# 4.971 1.771
# 1.000 1.000
# n=2 1 1 E 0.89 0.01
# 4.988
# 1.000
# H 1 # Label, l_shells, type (optional), ionic_charge (optional)
# 0 2 # l, Nzeta
# 5.00 0.00 # rc(izeta=1,Nzeta)(Bohr)
#H 2 0.22
# n=1 0 2 E 2.07 0.00
# 4.971 1.771
# 1.000 1.000
# n=2 1 1 E 0.89 0.01
# 4.988
# 1.000
# H 1
# 0 1
# 0. 0.8
## block below UNSURE
%block kgrid_Monkhorst_Pack
8 0 0 0.5
0 1 0 0.5
0 0 1 0.5
%endblock kgrid_Monkhorst_Pack
## is this the cutoff for the grid
## integration?
Lattice constant 5.66000 Ang
%block LatticeVectors
2.000 0.000 0.000
0.000 2.000 0.000
0.000 0.000 2.000
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
# output will be in cartesian angstroms
NumberOfAtoms 116
# CHANGE accordingly!
ZM.UnitsLength Ang
ZM.UnitsAngle deg
ZM.ForceTolLength 0.04 eV/Ang
# according to the paper for Si
MeshCutOff 200.0 Ry
# energy cut-off for 3D mesh
MaxSCFIterations 300
# was 100
DM.NumberPulay 8
# taken from the code for Si
# Pulay convergence accelerator
DM.Tolerance 0.1000000000E-02
#1.d-5 in Dani example
# 0.1000000000E-02 in siesta example
# when the in/out matrix difference
# reaches this number the procedure
# stops
SolutionMethod diagon
Diag.Memory 2.000000000
# default is 1.000000000
MD.VariableCell .true.
# if .true. lattice is relaxed together with
# the atomic coordinates in the
## conjugate gradient minimization.
# Allows to target hydrostatic pressures
# or arbitrary stress tensors.
MD.TypeOfRun CG
# coord optimization by conjugate
# gradients.
MD.UseSaveCG .true.
# .false. by default
MD.NumCGsteps 300
# 50 by default
MD.MaxCGDispl 0.1 ang
# .1 by default. Max displacement during
# relaxation.
# MD.MaxForceTol
# MD.MaxStressTol
WriteKpoints .false.
WriteDM .true.
# MAKE .false. for large molecules
WriteKbands .false.
# May have to CHANGE
WriteBands .false.
# May have to CHANGE
WriteCoorInitial .false.
# T by default
WriteMDXmol T
# Outputs a file for the XMol vizualization
# software.
LongOutput F
# F by default.
DirectPhi .false.
# SET to .true. if there is not enough
# memory.
WriteCoorXmol .false.
# Writes coordinates for Xmol software
WriteCoorCerius .false.
# Writes coordinates for Cerius
# vizualizator
# SET the above values to false if the
# files are useless.
%block AtomicCoordinatesAndAtomicSpecies
-3.001668 6.3675 0.000000 1 # Ge 1
-3.001668 1.965278 3.557533 1 # Ge 2
-3.001668 -2.436944 7.115066 1 # Ge 3
1.000556 4.480833 6.670374 1 # Ge 4
-3.001668 4.480833 6.670374 1 # Ge 5
-1.000556 5.424167 3.335187 1 # Ge 6
-1.000556 5.581389 5.780991 1 # Ge 7
-3.001668 6.524722 2.445804 1 # Ge 8
-1.000556 1.021944 6.89272 1 # Ge 9
-3.001668 2.1225 6.003337 1 # Ge 10
-3.001668 1.336389 -6.225682 1 # Ge 11
-3.001668 -3.065833 -2.66815 1 # Ge 12
-3.001668 -7.468056 0.889383 1 # Ge 13
1.000556 3.851944 -3.112841 1 # Ge 14
-3.001668 3.851944 -3.112841 1 # Ge 15
-1.000556 4.9525 -4.002224 1 # Ge 16
1.000556 -0.550278 0.444692 1 # Ge 17
-1.000556 2.908611 0.222346 1 # Ge 18
-3.001668 -0.550278 0.444692 1 # Ge 19
-1.000556 0.393056 -2.890495 1 # Ge 20
-1.000556 0.550278 -0.444692 1 # Ge 21
-3.001668 1.493611 -3.779879 1 # Ge 22
-3.001668 4.009167 -0.667037 1 # Ge 23
1.000556 -4.9525 4.002224 1 # Ge 24
-1.000556 -1.493611 3.779879 1 # Ge 25
-3.001668 -4.9525 4.002224 1 # Ge 26
-1.000556 -4.009167 0.667037 1 # Ge 27
-1.000556 -3.851944 3.112841 1 # Ge 28
-3.001668 -2.908611 -0.222346 1 # Ge 29
-3.001668 -0.393056 2.890495 1 # Ge 30
1.000556 6.3675 0.0 1 # Ge 31
-1.000556 7.468056 -0.889383 1 # Ge 32
3.001668 7.468056 -0.889383 1 # Ge 33
3.001668 5.424167 3.335187 1 # Ge 34
1.000556 1.965278 3.557533 1 # Ge 35
3.001668 2.908611 0.222346 1 # Ge 36
-1.000556 3.065833 2.66815 1 # Ge 37
3.001668 3.065833 2.66815 1 # Ge 38
1.000556 4.009167 -0.667037 1 # Ge 39
1.000556 6.524722 2.445804 1 # Ge 40
3.001668 1.021944 6.89272 1 # Ge 41
1.000556 -2.436944 7.115066 1 # Ge 42
3.001668 -1.493611 3.779879 1 # Ge 43
-1.000556 -1.336389 6.225682 1 # Ge 44
3.001668 -1.336389 6.225682 1 # Ge 45
1.000556 -0.393056 2.890495 1 # Ge 46
1.000556 2.1225 6.003337 1 # Ge 47
3.001668 5.581389 5.780991 1 # Ge 48
1.000556 -5.581389 -5.780991 1 # Ge 49
-1.000556 -2.1225 -6.003337 1 # Ge 50
-3.001668 -5.581389 -5.780991 1 # Ge 51
-1.000556 -4.480833 -6.670374 1 # Ge 52
-3.001668 -1.021944 -6.89272 1 # Ge 53
-1.000556 -6.524722 -2.445804 1 # Ge 54
-3.001668 -5.424167 -3.335187 1 # Ge 55
1.000556 1.336389 -6.225682 1 # Ge 56
-1.000556 2.436944 -7.115066 1 # Ge 57
3.001668 2.436944 -7.115066 1 # Ge 58
3.001668 0.393056 -2.890495 1 # Ge 59
1.000556 -3.065833 -2.66815 1 # Ge 60
3.001668 -2.1225 -6.003337 1 # Ge 61
-1.000556 -1.965278 -3.557533 1 # Ge 62
3.001668 -1.965278 -3.557533 1 # Ge 63
1.000556 -1.021944 -6.89272 1 # Ge 64
1.000556 1.493611 -3.779879 1 # Ge 65
3.001668 -4.009167 0.667037 1 # Ge 66
1.000556 -7.468056 0.889383 1 # Ge 67
3.001668 -6.524722 -2.445804 1 # Ge 68
-1.000556 -6.3675 0.000000 1 # Ge 69
3.001668 -6.3675 0.000000 1 # Ge 70
1.000556 -5.424167 -3.335187 1 # Ge 71
1.000556 -2.908611 -0.222346 1 # Ge 72
3.001668 4.9525 -4.002224 1 # Ge 73
3.001668 0.550278 -0.444692 1 # Ge 74
3.001668 -3.851944 3.112841 1 # Ge 75
3.001668 -4.480833 -6.670374 1 # Ge 76
-3.001668 -2.340582 8.614106 2 # H 77
-3.001668 -3.882374 6.706236 2 # H 78
1.000556 4.577195 8.169415 2 # H 79
-3.001668 4.577195 8.169415 2 # H 80
-1.000556 7.026819 6.18982 2 # H 81
-3.001668 7.970152 2.854633 2 # H 82
-1.000556 1.118306 8.391761 2 # H 83
-3.001668 -7.371694 2.388424 2 # H 84
-3.001668 -8.913486 0.480554 2 # H 85
-1.000556 6.39793 -3.593395 2 # H 86
-1.000556 4.856138 -5.501265 2 # H 87
1.000556 -4.856138 5.501265 2 # H 88
1.000556 -6.39793 3.593395 2 # H 89
-3.001668 -4.856138 5.501265 2 # H 90
-3.001668 -6.39793 3.593395 2 # H 91
-1.000556 8.913486 -0.480554 2 # H 92
-1.000556 7.371694 -2.388424 2 # H 93
3.001668 8.913486 -0.480554 2 # H 94
3.001668 7.371694 -2.388424 2 # H 95
1.000556 7.970152 2.854633 2 # H 96
3.001668 1.118306 8.391761 2 # H 97
1.000556 -2.340582 8.614106 2 # H 98
1.000556 -3.882374 6.706236 2 # H 99
3.001668 7.026819 6.18982 2 # H 100
1.000556 -7.026819 -6.18982 2 # H 101
-3.001668 -7.026819 -6.18982 2 # H 102
-1.000556 -4.577195 -8.169415 2 # H 103
-3.001668 -1.118306 -8.391761 2 # H 104
-1.000556 -7.970152 -2.854633 2 # H 105
-1.000556 3.882374 -6.706236 2 # H 106
-1.000556 2.340582 -8.614106 2 # H 107
3.001668 3.882374 -6.706236 2 # H 108
3.001668 2.340582 -8.614106 2 # H 109
1.000556 -1.118306 -8.391761 2 # H 110
1.000556 -7.371694 2.388424 2 # H 111
1.000556 -8.913486 0.480554 2 # H 112
3.001668 -7.970152 -2.854633 2 # H 113
3.001668 6.39793 -3.593395 2 # H 114
3.001668 4.856138 -5.501265 2 # H 115
3.001668 -4.577195 -8.169415 2 # H 116
%endblock AtomicCoordinatesAndAtomicSpecies
Ge.inp:
pg Germanium pseudopotential
tm2 3.0
n=Ge c=car
0.0 0.0 0.0 0.0 0.0 0.0
5 3
4 0 2.00 0.00
4 1 2.00 0.00
4 2 0.00 0.00
4 3 0.00 0.00
2.68 2.68 2.68
# pg Germanium pseudopotential
# tm2 3.0
#Ge car
# 0.0 0.0 0.0 0.0 0.0 0.0
# 5 3
# 4 0 2.00 0.00
# 4 1 2.00 0.00
# 4 2 0.00 0.00
# 4 3 0.00 0.00
# 1.81 2.26 0.51
#
# Last line (above):
# rc(s) rc(p) rc(d) rc(f) rcore_flag rcore
#
#23456789012345678901234567890123456789012345678901234567890
output message:
reinit: -----------------------------------------------------------------------
reinit: System Name: Hexagonal passivated GeNW
reinit: -----------------------------------------------------------------------
reinit: System Label: GeH
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Label: Ge Atomic number: 32
Species number: 2 Label: H Atomic number: 1
Ground state valence configuration: 4s02 4p02
Reading pseudopotential information in unformatted form from Ge.vps
Semicore shell(s) with 10 electrons included in the valence for
Ge
Ground state valence configuration: 1s01
Reading pseudopotential information in unformatted form from H.vps
relmxkb: Read Max KB Ang. Momentum= 2 for species Ge
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>
===============================================================================
Ge Z= 32 Mass= 72.610 Charge= 1.3403
Lmxo=2 Lmxkb=2 BasisType=split Semic=T
L=0 Nsemic=0 Cnfigmx=4
n=1 nzeta=2 polorb=0
vcte: 18.705
rinn: 5.9087
rcs: 7.1296 1.9242
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=4
n=1 nzeta=2 polorb=0
vcte: 81.005
rinn: 6.0512
rcs: 7.7152 4.9220
lambdas: 1.0000 1.0000
L=2 Nsemic=1 Cnfigmx=4
n=1 nzeta=2 polorb=0
vcte: 0.0000
rinn: 0.0000
rcs: 6.0000 5.0000
lambdas: 1.0000 1.0000
n=2 nzeta=1 polorb=0
vcte: 29.556
rinn: 5.2073
rcs: 7.7884
lambdas: 1.0000
-------------------------------------------------------------------------------
L=0 Nkbl=1 erefs: 0.17977+309
L=1 Nkbl=1 erefs: 0.17977+309
L=2 Nkbl=2 erefs: 0.17977+309 0.17977+309
===============================================================================
</basis_specs>
atom: Called for Ge (Z = 32)
read_vps: Pseudopotential generation method:
read_vps: ATM 3.2.2 Troullier-Martins
read_vps: Pseudopotential generated from a relativistic atomic calculation
read_vps: There are spin-orbit pseudopotentials available
read_vps: Spin-orbit interaction is not included in this calculation
read_vps: Valence configuration (pseudopotential and basis set generation):
4s( 2.00) rc: 1.10
4p( 2.00) rc: 1.13
4d( 0.00) rc: 1.17
Total valence charge: 4.00000
atom: Pseudopotential generated from an ionic configuration
atom: with net charge10.00
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.9576
V l=1 = -2*Zval/r beyond r= 1.9576
V l=2 = -2*Zval/r beyond r= 1.9576
All V_l potentials equal beyond r= 1.1580
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.9576
Using large-core scheme for Vlocal
atom: Estimated core radius 1.95761
atom: Including non-local core corrections could be a good idea
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.19072
atom: Maximum radius for r*vlocal+2*Zval: 1.98224
GHOST: WARNING: Ghost state for L = 0
GHOST: No ghost state for L = 1
KBgen: More than one KB projector for l= 2
KBgen: ghost states analysis will be not performed
KBgen: WARNING: Ghost states have been detected
KBgen: WARNING: Some parameter should be changed in the
KBgen: WARNING: pseudopotential generation procedure.
Stopping Program from Node: 0
GeH.fdf
Description: Binary data
Ge.tm2.inp
Description: Binary data
