Example execution error
I copied gfortran.make to arch.make and changed only FFFLAGS to "FFLAGS = -Og -g -pedantic -Wall -fcheck=all -fbacktrace -Warray-bounds -Wunused -Wuninitialized" I installed SIESTA with the arch.make and succeeded. Then I got H.psf and O.psf from the following site and put it on Example/H2O directory. http://nninc.cnf.cornell.edu/dd_search.php?frmxcprox=&frmxctype=&frmspclass=TM When I execute "siesta < h2o.fdf", I got the following error. I tried other some examples, but I got the same error "Error in code, non-full contained sp". I would appreciate it if you could tell me what is wrong.
Siesta Version : 5.0.0-alpha-19-g72dc1ecd6
Architecture : unknown
Compiler version: GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Compiler flags : gfortran -Og -g -pedantic -Wall -fcheck=all -fbacktrace -Warray-bounds -Wunused -Wuninitialized
PP flags : -DFC_HAVE_ABORT -DSIESTA__DIAG_2STAGE -DSIESTA__MRRR
Libraries : libsiestaLAPACK.a libsiestaBLAS.a
Parallelisations: none
Runtime information:
* Directory : /home/siesta/Examples/H2O
* Running in serial mode.
>> Start of run: 16-JAN-2022 8:03:27
***********************
* WELCOME TO SIESTA *
***********************
reinit: Reading from standard input
reinit: Dumping input in INPUT_TMP.09907
************************** Dump of input data file ****************************
SystemName Water molecule
SystemLabel h2o
NumberOfAtoms 3
NumberOfSpecies 2
%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
************************** End of input data file *****************************
reinit: -----------------------------------------------------------------------
reinit: System Name: Water molecule
reinit: -----------------------------------------------------------------------
reinit: System Label: h2o
reinit: -----------------------------------------------------------------------
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: 1.47
2p( 4.00) rc: 1.47
3d( 0.00) rc: 1.47
4f( 0.00) rc: 1.47
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.33
2p( 0.00) rc: 1.33
3d( 0.00) rc: 0.37
4f( 0.00) rc: 1.33
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
i=1 nzeta=2 polorb=0 (2s)
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
i=1 nzeta=2 polorb=1 (2p)
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: ATM 3.2.2 Troullier-Martins
Valence charge for ps generation: 6.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.3776
V l=1 = -2*Zval/r beyond r= 1.3776
V l=2 = -2*Zval/r beyond r= 1.3776
V l=3 = -2*Zval/r beyond r= 1.3776
All V_l potentials equal beyond r= 1.3776
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.3776
VLOCAL1: 99.0% of the norm of Vloc inside 22.873 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 52.129 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.66175
atom: Maximum radius for r*vlocal+2*Zval: 1.44823
KBgen: Kleinman-Bylander projectors:
GHOST: No ghost state for L = 0
l= 0 rc= 1.541657 el= -1.745026 Ekb= 5.003633 kbcos= 0.324143
GHOST: No ghost state for L = 1
l= 1 rc= 1.522502 el= -0.675318 Ekb= -7.282791 kbcos= -0.479019
GHOST: No ghost state for L = 2
l= 2 rc= 1.620715 el= 0.002270 Ekb= -1.583659 kbcos= -0.006017
GHOST: No ghost state for L = 3
l= 3 rc= 1.661751 el= 0.003337 Ekb= -0.631213 kbcos= -0.000757
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 = -1.726468
kinetic = 1.586990
potential(screened) = -3.313457
potential(ionic) = -11.299018
izeta = 2
rmatch = 2.510382
splitnorm = 0.150000
energy = -1.479190
kinetic = 2.383455
potential(screened) = -3.862646
potential(ionic) = -12.454133
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 = -0.657532
kinetic = 4.762562
potential(screened) = -5.420094
potential(ionic) = -13.167626
izeta = 2
rmatch = 2.541963
splitnorm = 0.150000
energy = -0.363029
kinetic = 7.131982
potential(screened) = -7.495011
potential(ionic) = -16.146258
POLgen: Perturbative polarization orbital with L= 2
POLgen: Polarization orbital for state 2p
izeta = 1
rc = 3.937239
energy = 2.397327
kinetic = 4.787558
potential(screened) = -2.390231
potential(ionic) = -8.704645
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
i=1 nzeta=2 polorb=1 (1s)
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: ATM 3.2.2 Troullier-Martins
Valence charge for ps generation: 1.00000
xc_check: Exchange-correlation functional:
xc_check: Ceperley-Alder
V l=0 = -2*Zval/r beyond r= 1.2656
V l=1 = -2*Zval/r beyond r= 1.2498
V l=2 = -2*Zval/r beyond r= 0.3563
All V_l potentials equal beyond r= 1.2656
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.2656
VLOCAL1: 99.0% of the norm of Vloc inside 27.100 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 61.762 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.48935
atom: Maximum radius for r*vlocal+2*Zval: 1.24984
KBgen: Kleinman-Bylander projectors:
GHOST: No ghost state for L = 0
l= 0 rc= 1.398961 el= -0.467364 Ekb= -1.985367 kbcos= -0.343724
GHOST: No ghost state for L = 1
l= 1 rc= 1.470814 el= 0.001361 Ekb= -0.479843 kbcos= -0.023156
GHOST: No ghost state for L = 2
l= 2 rc= 1.489346 el= 0.002250 Ekb= -0.476491 kbcos= -0.001599
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 = -0.449416
kinetic = 0.927973
potential(screened) = -1.377389
potential(ionic) = -1.913595
izeta = 2
rmatch = 3.854947
splitnorm = 0.150000
energy = -0.336198
kinetic = 1.502456
potential(screened) = -1.838653
potential(ionic) = -2.410667
POLgen: Perturbative polarization orbital with L= 1
POLgen: Polarization orbital for state 1s
izeta = 1
rc = 4.828263
energy = 0.707022
kinetic = 1.397353
potential(screened) = -0.690331
potential(ionic) = -1.170683
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: Matel table size (NRTAB) = 1024
redata: Mesh Cutoff = 300.0000 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 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: 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: ***********************************************************************
%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
siesta: k-grid: Number of k-points = 1
siesta: k-point is Gamma-only
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
ts: **************************************************************
ts: Save H and S matrices = 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
====================================
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=23 sparsity=1.0000 nnzs=529, refcount: 7>
<dData1D:(new from dSpData1D) n=529, 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=23 sparsity=1.0000 nnzs=529, refcount: 8>
<dData2D:DM n=529 m=1, refcount: 1>
refcount: 1>
No. of atoms with KB's overlaping orbs in proc 0. Max # of overlaps: 3 23
InitMesh: MESH = 80 x 60 x 60 = 288000
InitMesh: Mesh cutoff (required, used) = 300.000 301.251 Ry
New grid distribution [1]: sub = 2
stepf: Fermi-Dirac step function
siesta: Program's energy decomposition (eV):
siesta: Ebs = -82.527996
siesta: Eions = 674.103101
siesta: Ena = 85.209427
siesta: Ekin = 362.759172
siesta: Enl = -109.268851
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -13.965446
siesta: DUscf = 2.118207
siesta: DUext = 0.000000
siesta: Ex = -104.174641
siesta: Ec = -12.785654
siesta: Exc = -116.960295
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -466.012600
siesta: Etot = -464.210888
siesta: FreeEng = -464.210888
iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) dHmax(eV)
scf: 1 -466.012600 -464.210888 -464.210888 1.432624 -3.942269 7.298009
Error in code, non-full contained sp
Error in code, non-full contained sp
Stopping Program from Node: 0
Stopping Program from Node: 0
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
#0 0x7fd1d83a3d21 in ???
#1 0x7fd1d83a2ef5 in ???
#2 0x7fd1d806d20f in ???
#3 0x7fd1d806d18b in ???
#4 0x7fd1d804c858 in ???
#5 0x564e60e2960c in pxfabort_
at /home/siesta/Src/pxf.F90:95
#6 0x564e6095a6e4 in die_
at /home/siesta/Src/die.F:75
#7 0x564e60d2a73e in __io_sparse_m_MOD_io_write_sp
at /home/siesta/Src/io_sparse.F90:669
#8 0x564e6093acf8 in __m_iodm_MOD_write_dm
at /home/siesta/Src/m_iodm.F90:190
#9 0x564e6091602a in __m_save_density_matrix_MOD_save_density_matrix
at /home/siesta/Src/save_density_matrix.F90:142
#10 0x564e607d26af in __m_siesta_forces_MOD_siesta_forces
at /home/siesta/Src/siesta_forces.F90:448
#11 0x564e60e2a982 in siesta
at /home/siesta/Src/siesta.F:84
#12 0x564e60e2aa5e in main
at /home/siesta/Src/siesta.F:10
AbortedEdited by Nick R. Papior