Dear List
I am trying to optimize an organic molecule (cation) with DZP basis and GGA
psf
available freely from the Simune. My input is attached very below to this
mail.
Can any one tell why the program crashed even when I used Simunes' well
tested DZP basis and PSF files?
Simune: Are you able to reproduce this error? I use Siesta 4.1 in Linux 64.
Thanks in advance
Krishna
*******************************************************************
ERROR MESSAGE
*******************************************************************
....
....
************************** End of input data file
*****************************
reinit:
-----------------------------------------------------------------------
reinit: System Name: methyleneblue
reinit:
-----------------------------------------------------------------------
reinit: System Label: methbluegga
reinit:
-----------------------------------------------------------------------
initatom: Reading input for the pseudopotentials and atomic orbitals
----------
Species number: 1 Atomic number: 12 Label: C
Species number: 2 Atomic number: 1 Label: H
Species number: 3 Atomic number: 7 Label: N
Species number: 4 Atomic number: 16 Label: S
Ground state valence configuration: 3s02
Reading pseudopotential information in formatted form from C.psf
Pseudopotential generated from a relativistic atomic calculation
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.01
2p( 2.00) rc: 1.28
3d( 0.00) rc: 1.60
4f( 0.00) rc: 1.60
Ground state valence configuration: 1s01
Reading pseudopotential information in formatted form from H.psf
Pseudopotential generated from a relativistic atomic calculation
Valence configuration for pseudopotential generation:
1s( 1.00) rc: 1.31
2p( 0.00) rc: 1.13
3d( 0.00) rc: 1.09
4f( 0.00) rc: 1.14
Ground state valence configuration: 2s02 2p03
Reading pseudopotential information in formatted form from N.psf
Pseudopotential generated from a relativistic atomic calculation
Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.29
2p( 3.00) rc: 1.42
3d( 0.00) rc: 1.74
4f( 0.00) rc: 2.98
Ground state valence configuration: 3s02 3p04
Reading pseudopotential information in formatted form from S.psf
Pseudopotential generated from a relativistic atomic calculation
Valence configuration for pseudopotential generation:
3s( 2.00) rc: 1.35
3p( 4.00) rc: 2.04
3d( 0.00) rc: 1.92
4f( 0.00) rc: 1.80
Semicore shell(s) with 2 electrons included in the valence for
C
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.
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.
For N, 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 S, 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= 12 Mass= 24.310 Charge= 0.17977+309
Lmxo=2 Lmxkb= 3 BasisType=split Semic=T
L=0 Nsemic=0 Cnfigmx=2
n=1 nzeta=2 polorb=0
splnorm: 0.15000
vcte: 40.000
rinn: -0.90000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 5.9487 2.5090
lambdas: 1.0000 1.0000
L=1 Nsemic=0 Cnfigmx=2
n=1 nzeta=2 polorb=0
splnorm: 0.15000
vcte: 40.000
rinn: -0.90000
qcoe: 0.0000
qyuk: 0.0000
qwid: 0.10000E-01
rcs: 7.6384 2.6226
lambdas: 1.0000 1.0000
L=2 Nsemic=0 Cnfigmx=2
n=1 nzeta=1 polorb=0
splnorm: 0.15000
vcte: 40.000
rinn: -0.90000
qcoe: 6.4005
qyuk: 0.10000E-01
qwid: 0.10000E-01
rcs: 7.6384
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 = 12)
read_vps: Pseudopotential generation method:
read_vps: ATM4.1.0 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: GGA Perdew, Burke & Ernzerhof 1996
V l=0 = -2*Zval/r beyond r= 1.3105
V l=1 = -2*Zval/r beyond r= 1.3437
V l=2 = -2*Zval/r beyond r= 1.5809
V l=3 = -2*Zval/r beyond r= 1.5612
All V_l potentials equal beyond r= 1.5612
This should be close to max(r_c) in ps generation
All pots = -2*Zval/r beyond r= 1.5809
VLOCAL1: 99.0% of the norm of Vloc inside 17.809 Ry
VLOCAL1: 99.9% of the norm of Vloc inside 40.586 Ry
atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.88329
atom: Maximum radius for r*vlocal+2*Zval: 1.62091
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= 1.725473 el= -1.010221 Ekb= 8.218425 kbcos= 0.222598
l= 1 rc= 1.725473 el= -0.388552 Ekb= -5.584060 kbcos= -0.323429
l= 2 rc= 2.055542 el= 0.001971 Ekb= -0.907290 kbcos= -0.010017
l= 3 rc= 2.300349 el= 0.003065 Ekb= -0.378353 kbcos= -0.001367
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 = 5.948690
energy = -1.009571
kinetic = 0.879711
potential(screened) = -1.889282
potential(ionic) = -5.431187
izeta = 2
rmatch = 2.542323
splitnorm = 0.464849
energy = -0.304021
kinetic = 2.397087
potential(screened) = -2.701108
potential(ionic) = -6.677248
SPLIT: Orbitals with angular momentum L= 1
SPLIT: Basis orbitals for state 2p
izeta = 1
lambda = 1.000000
rc = 7.638387
energy = -0.387791
kinetic = 2.366378
potential(screened) = -2.754169
potential(ionic) = -6.141387
izeta = 2
rmatch = 2.606692
splitnorm = 0.403257
energy = 0.178602
kinetic = 5.443206
potential(screened) = -5.264603
potential(ionic) = -9.357889
SPLIT: Orbitals with angular momentum L= 2
SPLIT: Basis orbitals for state 2d
Charge confinement: Q: 6.4005
izeta = 1
lambda = 1.000000
rc = 7.638387
energy = 1.876278
kinetic = 3.712261
potential(screened) = -1.835983
potential(ionic) = -5.109537
atom: Total number of Sankey-type orbitals: 13
atm_pop: Valence configuration (for local Pseudopot. screening):
2s( 2.00) 0s( 2.00)
2p( 6.00) 0p( 0.00)
2d(10.00) 0d( 0.00)
Vna: chval, zval: 18.00000 4.00000
You might have an extra low-lying basis orbital
Total charge in occupied basis states different from valence charge
Total charge in occupied basis states different from valence charge
Stopping Program from Node: 0
Stopping Program from Node: 0
Program aborted. Backtrace:
#0 0x150f52117640 in ???
#1 0x150f52118134 in ???
#2 0x150f52292f08 in ???
#3 0x7fe10a in ???
#4 0x4e5349 in vna
at /home/krishnamohan/MyScience/Siesta/siesta-4.1-b4/Src/atom.F:5421
#5 0x4fcbcc in __atom_MOD_atom_main
at /home/krishnamohan/MyScience/Siesta/siesta-4.1-b4/Src/atom.F:656
#6 0x44b669 in ???
#7 0x4b4567 in ???
#8 0x402bae in ???
#9 0x150f515cb349 in ???
#10 0x402c79 in ???
at ../sysdeps/x86_64/start.S:120
#11 0xffffffffffffffff in ???
Aborted (core dumped)
*************************************************************************
INPUT FILE
**************************************************************************
SystemName methyleneblue
SystemLabel methbluegga
NumberOfSpecies 4
NumberOfAtoms 38
%block ChemicalSpeciesLabel
1 12 C
2 1 H
3 7 N
4 16 S
%endblock ChemicalSpeciesLabel
PAO.BasisType split
PAO.BasisSize DZP
PAO.EnergyShift 0.02 Ry
%block PAO.Basis
C 3
n=2 0 2 E 40 -0.9
5.94869034392 2.5090419
n=2 1 2 E 40 -0.9
7.63838693570 2.6226139
n=2 2 1 E 40 -0.9 Q 6.4005365 .0100000
7.63838693570
H 2
n=1 0 2 E 40 -0.9
7.38657734676 2.5578156
n=1 1 1 E 40 -0.9 Q 9.4900562 1.5464743
7.38657734676
N 3
n=2 0 2 E 40 -0.9
6.5 4.3806496
n=2 1 2 E 40 -0.9
6.71294063991 2.4269315
n=2 2 1 E 40 -0.9 Q 8.2241579 .0100000
6.71294063991
S 3
n=3 0 2 E 40 -0.9
5.76834044229 3.3526650
n=3 1 2 E 40 -0.9
7.40673974180 3.5873572
n=3 2 1 E 40 -0.9 Q 2.6112698 .0100000
7.40673974180
%endblock PAO.Basis
XC.Functional GGA
XC.authors PBE
LatticeConstant 1 Ang
%block LatticeVectors
40.00000 0.000000 0.000000
0.000000 40.00000 0.000000
0.000000 0.000000 40.00000
%endblock LatticeVectors
%block kgrid_Monkhorst_Pack
6 0 0 0.5
0 6 0 0.5
0 0 6 0.5
%endblock kgrid_Monkhorst_Pack
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
-1.3751 -0.4797 -0.0229 1
1.3545 -0.3909 -0.0146 1
-1.1741 0.9951 0.0433 1
1.1889 0.9956 0.0470 1
-3.8132 -0.1564 -0.0134 1
3.7732 -0.1081 0.0013 1
-2.6075 -1.0066 -0.0489 1
2.6504 -0.9339 -0.0370 1
-2.4101 1.8260 0.0787 1
2.3299 1.8145 0.0849 1
-3.6360 1.3017 0.0525 1
3.6128 1.2695 0.0624 1
-5.1847 -2.1463 -0.1081 1
-6.2100 0.1677 -0.0087 1
6.1714 0.0561 -0.6161 1
5.3100 -1.9764 0.5567 1
-2.7154 -2.0853 -0.0973 2
2.7674 -2.0142 -0.0983 2
-2.2828 2.9033 0.1275 2
2.2200 2.8961 0.1355 2
-4.4809 1.9788 0.0815 2
4.4602 1.9473 0.1054 2
-4.7433 -2.6060 0.7809 2
-4.7387 -2.5245 -1.0324 2
-6.2532 -2.3785 -0.1211 2
-6.2167 0.8199 -0.8868 2
-6.2252 0.7367 0.9253 2
-7.1008 -0.4656 -0.0421 2
6.5551 0.8121 0.0769 2
5.8755 0.5438 -1.5518 2
7.0002 -0.6176 -0.8611 2
4.7795 -2.0989 1.5079 2
6.3751 -2.1211 0.7697 2
5.0014 -2.7703 -0.1315 2
-4.9874 -0.6754 -0.0415 3
5.0658 -0.6703 -0.0232 3
-0.0519 1.6424 0.0741 3
-0.0068 -1.5248 -0.0665 4
%endblock AtomicCoordinatesAndAtomicSpecies
# Cation = +1 charge!
NetCharge = 1.
kgrid_cutoff 50.0 Ang
MD.TypeOfRun CG
MD.VariableCell T
MD.NumCGsteps 200
MD.MaxCGDispl 0.05 Ang
MD.MaxForceTol 0.005 eV/Ang # 5.d-5 eV/Ang
MeshCutoff 300 Ry
DM.NumberPulay 7
DM.UseSaveDM F
DM.MixingWeight 0.5000 # New DM amount for next SCF cycle
DM.Tolerance 1.d-6 # Tolerance in maximum difference
# between input and output DM
DM.NumberKick 5
DM.KickMixingWeight 1.000
DM.RequireEnergyConvergence T
DM.EnergyTolerance 1.d-7 Ry
ElectronicTemperature 300 K
MaxSCFIterations 100
WriteCoorStep .true.
WriteForces .true.
WriteKpoints .false.
--
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