Dear siesta users, I’m trying to converge several parameters for a (10,0) CNT with 3 unit cells. I’m having trouble getting the calculations to work properly (which wasn’t the case for a single unit cell). I get segmentation fault errors when the routine is initializing the density matrix. I attached the siesta output (.txt). I’ve also attached an input file. I’ve checked my geometry with xcrysden, after using the xv2xsf utility, and it seems fine.
I was wondering if someone is able to reproduce my error, to see if there is a problem with the compilation of the version I’m using (4.0). If it is the case, I will have to talk to my system administrator or compile the program myself. I use 4 processors in parallel with mpirun. Thank you in advance, Nicolas Duchêne Master’s student at École Polytechnique de Montréal
1000CNT_PBE_1_20_500.fdf
Description: Binary data
Siesta Version: siesta-3.1
Architecture : x86_64-unknown-linux-gnu--Intel
Compiler flags: mpif90 -g -O2
PARALLEL version
* Running on 4 nodes in parallel
>> Start of run: 2-JUN-2017 11:10:53
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
************************** Dump of input data file ****************************
SystemName 1000CNT_PBE_1_20_500
SystemLabel 1000CNT_PBE_1_20_500
NumberOfAtoms 120
NumberOfSpecies 1
%block ChemicalSpeciesLabel
1 6 C
%endblock ChemicalSpeciesLabel
LatticeConstant 12.802164 Ang
%block LatticeVectors
1.22769556772 0.0 0.0
0.0 1.22769556772 0.0
0.0 0.0 1.0
%endblock LatticeVectors
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
11.78787 7.85858 1.777347 1
11.78787 7.85858 0.356347 1
11.595556 9.072797 3.911041 1
11.595556 9.072797 2.490041 1
11.037442 10.168158 1.777347 1
11.037442 10.168158 0.356347 1
10.168158 11.037442 3.911041 1
10.168158 11.037442 2.490041 1
9.072797 11.595556 1.777347 1
9.072797 11.595556 0.356347 1
7.85858 11.78787 3.911041 1
7.85858 11.78787 2.490041 1
6.644363 11.595556 1.777347 1
6.644363 11.595556 0.356347 1
5.549002 11.037442 3.911041 1
5.549002 11.037442 2.490041 1
4.679718 10.168158 1.777347 1
4.679718 10.168158 0.356347 1
4.121604 9.072797 3.911041 1
4.121604 9.072797 2.490041 1
3.92929 7.85858 1.777347 1
3.92929 7.85858 0.356347 1
4.121604 6.644363 3.911041 1
4.121604 6.644363 2.490041 1
4.679718 5.549002 1.777347 1
4.679718 5.549002 0.356347 1
5.549002 4.679718 3.911041 1
5.549002 4.679718 2.490041 1
6.644363 4.121604 1.777347 1
6.644363 4.121604 0.356347 1
7.85858 3.92929 3.911041 1
7.85858 3.92929 2.490041 1
9.072797 4.121604 1.777347 1
9.072797 4.121604 0.356347 1
10.168158 4.679718 3.911041 1
10.168158 4.679718 2.490041 1
11.037442 5.549002 1.777347 1
11.037442 5.549002 0.356347 1
11.595556 6.644363 3.911041 1
11.595556 6.644363 2.490041 1
11.78787 7.85858 6.044735 1
11.78787 7.85858 4.623735 1
11.595556 9.072797 8.178429 1
11.595556 9.072797 6.757429 1
11.037442 10.168158 6.044735 1
11.037442 10.168158 4.623735 1
10.168158 11.037442 8.178429 1
10.168158 11.037442 6.757429 1
9.072797 11.595556 6.044735 1
9.072797 11.595556 4.623735 1
7.85858 11.78787 8.178429 1
7.85858 11.78787 6.757429 1
6.644363 11.595556 6.044735 1
6.644363 11.595556 4.623735 1
5.549002 11.037442 8.178429 1
5.549002 11.037442 6.757429 1
4.679718 10.168158 6.044735 1
4.679718 10.168158 4.623735 1
4.121604 9.072797 8.178429 1
4.121604 9.072797 6.757429 1
3.92929 7.85858 6.044735 1
3.92929 7.85858 4.623735 1
4.121604 6.644363 8.178429 1
4.121604 6.644363 6.757429 1
4.679718 5.549002 6.044735 1
4.679718 5.549002 4.623735 1
5.549002 4.679718 8.178429 1
5.549002 4.679718 6.757429 1
6.644363 4.121604 6.044735 1
6.644363 4.121604 4.623735 1
7.85858 3.92929 8.178429 1
7.85858 3.92929 6.757429 1
9.072797 4.121604 6.044735 1
9.072797 4.121604 4.623735 1
10.168158 4.679718 8.178429 1
10.168158 4.679718 6.757429 1
11.037442 5.549002 6.044735 1
11.037442 5.549002 4.623735 1
11.595556 6.644363 8.178429 1
11.595556 6.644363 6.757429 1
11.78787 7.85858 10.312123 1
11.78787 7.85858 8.891123 1
11.595556 9.072797 12.445817 1
11.595556 9.072797 11.024817 1
11.037442 10.168158 10.312123 1
11.037442 10.168158 8.891123 1
10.168158 11.037442 12.445817 1
10.168158 11.037442 11.024817 1
9.072797 11.595556 10.312123 1
9.072797 11.595556 8.891123 1
7.85858 11.78787 12.445817 1
7.85858 11.78787 11.024817 1
6.644363 11.595556 10.312123 1
6.644363 11.595556 8.891123 1
5.549002 11.037442 12.445817 1
5.549002 11.037442 11.024817 1
4.679718 10.168158 10.312123 1
4.679718 10.168158 8.891123 1
4.121604 9.072797 12.445817 1
4.121604 9.072797 11.024817 1
3.92929 7.85858 10.312123 1
3.92929 7.85858 8.891123 1
4.121604 6.644363 12.445817 1
4.121604 6.644363 11.024817 1
4.679718 5.549002 10.312123 1
4.679718 5.549002 8.891123 1
5.549002 4.679718 12.445817 1
5.549002 4.679718 11.024817 1
6.644363 4.121604 10.312123 1
6.644363 4.121604 8.891123 1
7.85858 3.92929 12.445817 1
7.85858 3.92929 11.024817 1
9.072797 4.121604 10.312123 1
9.072797 4.121604 8.891123 1
10.168158 4.679718 12.445817 1
10.168158 4.679718 11.024817 1
11.037442 5.549002 10.312123 1
11.037442 5.549002 8.891123 1
11.595556 6.644363 12.445817 1
11.595556 6.644363 11.024817 1
%endblock AtomicCoordinatesAndAtomicSpecies
%block PAO.Basis
C 3
0 2
4.067 2.220
1 2
5.782 3.641
2 1
3.395
%endblock PAO.Basis
%block kgrid_Monkhorst_Pack
1 0 0 0.5
0 1 0 0.5
0 0 20 0.5
%endblock kgrid_Monkhorst_Pack
MeshCutOff 500 Ry
XC.Functional GGA
XC.authors PBE
MaxSCFIterations 250
DM.NumberBroyden 3
DM.MixingWeight 0.01 # New DM amount for next SCF cycle
DM.Tolerance 0.001 # Tolerance in maximum difference
DM.UseSaveDM .false. # to use continuation files
DM.NumberKick 100
DM.KickMixingWeight 0.01
BandLinesScale pi/a
%block BandPoints
0.0000 0.0000 0.0000 #/Gamma
%endblock BandPoints
ElectronicTemperature 300 K
# MD entry
SaveRho .true.
SaveDeltaRho .true.
#%block ProjectedDensityOfStates
# -10.0 2.0 0.01 500 eV
#%endblock ProjectedDensityOfStates
# %block LocalDensityOfStates
# -10.0 2.0 eV
# %endblock LocalDensityOfStates
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: 1000CNT_PBE_1_20_500
reinit: -----------------------------------------------------------------------
reinit: System Label: 1000CNT_PBE_1_20_500
reinit: -----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number: 1 Label: C Atomic number: 6
Ground state valence configuration: 2s02 2p02
Reading pseudopotential information in formatted form from C.psf
Pseudopotential generated from a relativistic atomic calculation
There are spin-orbit pseudopotentials available
Spin-orbit interaction is not included in this calculation
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.84
2p( 2.00) rc: 1.62
3d( 0.00) rc: 1.64
4f( 0.00) rc: 1.58
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.
<basis_specs>
===============================================================================
C Z= 6 Mass= 12.010 Charge= 0.17977+309
Lmxo=2 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
rcs: 4.0670 2.2200
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
n=1 nzeta=2 polorb=0
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
rcs: 5.7820 3.6410
lambdas: 1.0000 1.0000
L=2 Nsemic=0 Cnfigmx=3
n=1 nzeta=1 polorb=0
splnorm: 0.15000
vcte: 0.0000
rinn: 0.0000
rcs: 3.3950
lambdas: 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 C (Z = 6)
read_vps: Pseudopotential generation method:
read_vps: ATM3 Troullier-Martins
Total valence charge: 4.00000
xc_check: Exchange-correlation functional:
xc_check: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 1.8140
V l=1 = -2*Zval/r beyond r= 1.7692
V l=2 = -2*Zval/r beyond r= 1.7692
V l=3 = -2*Zval/r beyond r= 1.7692
All V_l potentials equal beyond r= 1.8140
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.8140
VLOCAL1: 99.0% of the norm of Vloc inside 13.192 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 30.065 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 2.16095
atom: Maximum radius for r*vlocal+2*Zval: 1.88329
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= 2.004780 el= -1.010207 Ekb= 2.995585 kbcos= 0.335322
l= 1 rc= 1.979871 el= -0.388556 Ekb= -4.412411 kbcos= -0.405487
l= 2 rc= 2.188140 el= 0.001971 Ekb= -1.183708 kbcos= -0.012464
l= 3 rc= 2.479542 el= 0.003065 Ekb= -0.600911 kbcos= -0.001805
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
izeta = 1
lambda = 1.000000
rc = 4.088342
energy = -0.989536
kinetic = 0.885538
potential(screened) = -1.875075
potential(ionic) = -5.504772
izeta = 2
rmatch = 2.243543
splitnorm = 0.599101
energy = -0.071374
kinetic = 2.345293
potential(screened) = -2.416668
potential(ionic) = -6.546927
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 2p
izeta = 1
lambda = 1.000000
rc = 5.801806
energy = -0.382200
kinetic = 2.365524
potential(screened) = -2.747724
potential(ionic) = -6.185392
izeta = 2
rmatch = 3.699245
splitnorm = 0.145037
energy = -0.248893
kinetic = 3.510160
potential(screened) = -3.759053
potential(ionic) = -7.578780
SPLIT: Orbitals with angular momentum L= 2
SPLIT: Basis orbitals for state 3d
izeta = 1
lambda = 1.000000
rc = 3.431921
energy = 1.775400
kinetic = 2.977121
potential(screened) = -1.201720
potential(ionic) = -4.245406
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: 5.801806
atom: _________________________________________________________________________
prinput: Basis input ----------------------------------------------------------
PAO.BasisType split
%block ChemicalSpeciesLabel
1 6 C # Species index, atomic number, species label
%endblock ChemicalSpeciesLabel
%block PAO.Basis # Define Basis set
C 3 # Species label, number of l-shells
n=2 0 2 # n, l, Nzeta
4.088 2.244
1.000 1.000
n=2 1 2 # n, l, Nzeta
5.802 3.699
1.000 1.000
n=3 2 1 # n, l, Nzeta
3.432
1.000
%endblock PAO.Basis
prinput: ----------------------------------------------------------------------
coor: Atomic-coordinates input format = Cartesian coordinates
coor: (in Angstroms)
siesta: Atomic coordinates (Bohr) and species
siesta: 22.27585 14.85057 3.35870 1 1
siesta: 22.27585 14.85057 0.67340 1 2
siesta: 21.91243 17.14511 7.39080 1 3
siesta: 21.91243 17.14511 4.70550 1 4
siesta: 20.85775 19.21504 3.35870 1 5
siesta: 20.85775 19.21504 0.67340 1 6
siesta: 19.21504 20.85775 7.39080 1 7
siesta: 19.21504 20.85775 4.70550 1 8
siesta: 17.14511 21.91243 3.35870 1 9
siesta: 17.14511 21.91243 0.67340 1 10
siesta: 14.85057 22.27585 7.39080 1 11
siesta: 14.85057 22.27585 4.70550 1 12
siesta: 12.55603 21.91243 3.35870 1 13
siesta: 12.55603 21.91243 0.67340 1 14
siesta: 10.48610 20.85775 7.39080 1 15
siesta: 10.48610 20.85775 4.70550 1 16
siesta: 8.84339 19.21504 3.35870 1 17
siesta: 8.84339 19.21504 0.67340 1 18
siesta: 7.78871 17.14511 7.39080 1 19
siesta: 7.78871 17.14511 4.70550 1 20
siesta: 7.42528 14.85057 3.35870 1 21
siesta: 7.42528 14.85057 0.67340 1 22
siesta: 7.78871 12.55603 7.39080 1 23
siesta: 7.78871 12.55603 4.70550 1 24
siesta: 8.84339 10.48610 3.35870 1 25
siesta: 8.84339 10.48610 0.67340 1 26
siesta: 10.48610 8.84339 7.39080 1 27
siesta: 10.48610 8.84339 4.70550 1 28
siesta: 12.55603 7.78871 3.35870 1 29
siesta: 12.55603 7.78871 0.67340 1 30
siesta: 14.85057 7.42528 7.39080 1 31
siesta: 14.85057 7.42528 4.70550 1 32
siesta: 17.14511 7.78871 3.35870 1 33
siesta: 17.14511 7.78871 0.67340 1 34
siesta: 19.21504 8.84339 7.39080 1 35
siesta: 19.21504 8.84339 4.70550 1 36
siesta: 20.85775 10.48610 3.35870 1 37
siesta: 20.85775 10.48610 0.67340 1 38
siesta: 21.91243 12.55603 7.39080 1 39
siesta: 21.91243 12.55603 4.70550 1 40
siesta: 22.27585 14.85057 11.42290 1 41
siesta: 22.27585 14.85057 8.73760 1 42
siesta: 21.91243 17.14511 15.45500 1 43
siesta: 21.91243 17.14511 12.76970 1 44
siesta: 20.85775 19.21504 11.42290 1 45
siesta: 20.85775 19.21504 8.73760 1 46
siesta: 19.21504 20.85775 15.45500 1 47
siesta: 19.21504 20.85775 12.76970 1 48
siesta: 17.14511 21.91243 11.42290 1 49
siesta: 17.14511 21.91243 8.73760 1 50
siesta: 14.85057 22.27585 15.45500 1 51
siesta: 14.85057 22.27585 12.76970 1 52
siesta: 12.55603 21.91243 11.42290 1 53
siesta: 12.55603 21.91243 8.73760 1 54
siesta: 10.48610 20.85775 15.45500 1 55
siesta: 10.48610 20.85775 12.76970 1 56
siesta: 8.84339 19.21504 11.42290 1 57
siesta: 8.84339 19.21504 8.73760 1 58
siesta: 7.78871 17.14511 15.45500 1 59
siesta: 7.78871 17.14511 12.76970 1 60
siesta: 7.42528 14.85057 11.42290 1 61
siesta: 7.42528 14.85057 8.73760 1 62
siesta: 7.78871 12.55603 15.45500 1 63
siesta: 7.78871 12.55603 12.76970 1 64
siesta: 8.84339 10.48610 11.42290 1 65
siesta: 8.84339 10.48610 8.73760 1 66
siesta: 10.48610 8.84339 15.45500 1 67
siesta: 10.48610 8.84339 12.76970 1 68
siesta: 12.55603 7.78871 11.42290 1 69
siesta: 12.55603 7.78871 8.73760 1 70
siesta: 14.85057 7.42528 15.45500 1 71
siesta: 14.85057 7.42528 12.76970 1 72
siesta: 17.14511 7.78871 11.42290 1 73
siesta: 17.14511 7.78871 8.73760 1 74
siesta: 19.21504 8.84339 15.45500 1 75
siesta: 19.21504 8.84339 12.76970 1 76
siesta: 20.85775 10.48610 11.42290 1 77
siesta: 20.85775 10.48610 8.73760 1 78
siesta: 21.91243 12.55603 15.45500 1 79
siesta: 21.91243 12.55603 12.76970 1 80
siesta: 22.27585 14.85057 19.48710 1 81
siesta: 22.27585 14.85057 16.80179 1 82
siesta: 21.91243 17.14511 23.51919 1 83
siesta: 21.91243 17.14511 20.83389 1 84
siesta: 20.85775 19.21504 19.48710 1 85
siesta: 20.85775 19.21504 16.80179 1 86
siesta: 19.21504 20.85775 23.51919 1 87
siesta: 19.21504 20.85775 20.83389 1 88
siesta: 17.14511 21.91243 19.48710 1 89
siesta: 17.14511 21.91243 16.80179 1 90
siesta: 14.85057 22.27585 23.51919 1 91
siesta: 14.85057 22.27585 20.83389 1 92
siesta: 12.55603 21.91243 19.48710 1 93
siesta: 12.55603 21.91243 16.80179 1 94
siesta: 10.48610 20.85775 23.51919 1 95
siesta: 10.48610 20.85775 20.83389 1 96
siesta: 8.84339 19.21504 19.48710 1 97
siesta: 8.84339 19.21504 16.80179 1 98
siesta: 7.78871 17.14511 23.51919 1 99
siesta: 7.78871 17.14511 20.83389 1 100
siesta: 7.42528 14.85057 19.48710 1 101
siesta: 7.42528 14.85057 16.80179 1 102
siesta: 7.78871 12.55603 23.51919 1 103
siesta: 7.78871 12.55603 20.83389 1 104
siesta: 8.84339 10.48610 19.48710 1 105
siesta: 8.84339 10.48610 16.80179 1 106
siesta: 10.48610 8.84339 23.51919 1 107
siesta: 10.48610 8.84339 20.83389 1 108
siesta: 12.55603 7.78871 19.48710 1 109
siesta: 12.55603 7.78871 16.80179 1 110
siesta: 14.85057 7.42528 23.51919 1 111
siesta: 14.85057 7.42528 20.83389 1 112
siesta: 17.14511 7.78871 19.48710 1 113
siesta: 17.14511 7.78871 16.80179 1 114
siesta: 19.21504 8.84339 23.51919 1 115
siesta: 19.21504 8.84339 20.83389 1 116
siesta: 20.85775 10.48610 19.48710 1 117
siesta: 20.85775 10.48610 16.80179 1 118
siesta: 21.91243 12.55603 23.51919 1 119
siesta: 21.91243 12.55603 20.83389 1 120
siesta: System type = chain
initatomlists: Number of atoms, orbitals, and projectors: 120 1560 1920
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: Non-Collinear-spin run = F
redata: SpinPolarized (Up/Down) run = F
redata: Number of spin components = 1
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: Mesh Cutoff = 500.0000 Ry
redata: Net charge of the system = 0.0000 |e|
redata: Max. number of SCF Iter = 250
redata: Broyden mixing with 3 saved histories.
redata: Mix DM in first SCF step ? = F
redata: Write Pulay info on disk? = F
redata: Discard 1st Pulay DM after kick = F
redata: New DM Mixing Weight = 0.0100
redata: New DM Occupancy tolerance = 0.000000000001
redata: Kick with linear mixing every = 100 iterations
redata: DM Mixing Weight for Kicks = 0.0100
redata: DM Tolerance for SCF = 0.001000
redata: Require Energy convergence for SCF = F
redata: DM Energy tolerance for SCF = 0.000100 eV
redata: Require Harris convergence for SCF = F
redata: DM Harris 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 = 0.0019 Ry
redata: Fix the spin of the system = F
redata: Dynamics option = Verlet MD run
redata: Initial MD time step = 1
redata: Final MD time step = 1
redata: Length of MD time step = 1.0000 fs
redata: Initial Temperature of MD run = 0.0000 K
redata: Perform a MD quench = F
redata: ***********************************************************************
Total number of electrons: 480.000000
Total ionic charge: 480.000000
* ProcessorY, Blocksize: 2 24
k-point displ. along 1 input, could be: 0.50 0.00
k-point displ. along 2 input, could be: 0.50 0.00
Kpoints in: 10 . Kpoints trimmed: 10
siesta: k-grid: Number of k-points = 10
siesta: k-grid: Cutoff (effective) = 7.859 Ang
siesta: k-grid: Supercell and displacements
siesta: k-grid: 1 0 0 0.500
siesta: k-grid: 0 1 0 0.500
siesta: k-grid: 0 0 20 0.500
Naive supercell factors: 2 2 2
superc: Internal auxiliary supercell: 2 x 2 x 2 = 8
superc: Number of atoms, orbitals, and projectors: 960 12480 15360
* Maximum dynamic memory allocated = 2 MB
siesta: ==============================
Begin MD step = 1
==============================
superc: Internal auxiliary supercell: 2 x 2 x 2 = 8
superc: Number of atoms, orbitals, and projectors: 960 12480 15360
outcell: Unit cell vectors (Ang):
15.717160 0.000000 0.000000
0.000000 15.717160 0.000000
0.000000 0.000000 12.802164
outcell: Cell vector modules (Ang) : 15.717160 15.717160 12.802164
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 3162.5073
New_DM. Step: 1
Initializing Density Matrix...
InitMesh: MESH = 216 x 216 x 180 = 8398080
InitMesh: Mesh cutoff (required, used) = 500.000 521.989 Ry
