Dear List
I am trying to calculate the optical spectrum of a Zeolite compound and we have its experimental spectrum and it shows a clear absorption in Visible region (and the pure Zeolite compound is a colored one). So we expect that the Siesta’s spectrum would reflect this too.
But when I tried the calculation (Pls see below part) it runs and completed SCF cycle and it seems it stuck in the portion:
130 -0.012952 -0.089863 0.127418
131 0.020422 0.101546 -0.046036
132 0.047941 -0.009764 0.000107
133 -0.043814 -0.020094 -0.131299
134 -0.056622 0.062521 0.031526
135 0.042265 -0.027729 -0.004018
136 -0.016008 0.021773 0.020389
137 0.063636 -0.039750 -0.033829
138 0.055053 0.033202 -0.021522
Tot -0.005242 0.008209 -0.009872
Max 0.337362
Res 0.065680 sqrt( Sum f_i^2 / 3N )
Max 0.337362 constrained
Stress tensor Voigt[x,y,z,yz,xz,xy] (kbar): 2.89 2.86 1.82 -0.46 -0.58 -0.51
(Free)E + p*V (eV/cell) -19533.6875
Target enthalpy (eV/cell) -19529.8878
coxmol: Writing XMOL coordinates into file zif67optical.xyz
siesta: Program’s energy decomposition (eV):
siesta: Ebs = -5482.245303
siesta: Eions = 23083.627097
siesta: Ena = 3227.550941
siesta: Ekin = 16297.878613
siesta: Enl = -9828.161993
siesta: Eso = 0.000000
siesta: Edftu = 0.000000
siesta: DEna = -413.734991
siesta: DUscf = 64.552342
siesta: DUext = 0.000000
siesta: Exc = -5794.300663
siesta: eta*DQ = 0.000000
siesta: Emadel = 0.000000
siesta: Emeta = 0.000000
siesta: Emolmec = 0.000000
siesta: Ekinion = 0.000000
siesta: Eharris = -19529.842846
siesta: Etot = -19529.842848
siesta: FreeEng = -19529.887822
siesta: Final energy (eV):
siesta: Band Struct. = -5482.245303
siesta: Kinetic = 16297.878613
siesta: Hartree = 30900.513857
siesta: Edftu = 0.000000
siesta: Eso = 0.000000
siesta: Ext. field = 0.000000
siesta: Exch.-corr. = -5794.300663
siesta: Ion-electron = -76563.859626
siesta: Ion-ion = 15629.924971
siesta: Ekinion = 0.000000
siesta: Total = -19529.842848
siesta: Fermi = -4.707019
siesta: Atomic forces (eV/Ang):
siesta: 1 -0.026727 0.000182 -0.015051
siesta: 2 0.044114 -0.043744 -0.001681
siesta: 3 0.020104 -0.007544 -0.115776
siesta: 4 0.054796 -0.053486 -0.025071
…
…
siesta: 129 -0.036863 -0.041463 -0.047218
siesta: 130 -0.012952 -0.089863 0.127418
siesta: 131 0.020422 0.101546 -0.046036
siesta: 132 0.047941 -0.009764 0.000107
siesta: 133 -0.043814 -0.020094 -0.131299
siesta: 134 -0.056622 0.062521 0.031526
siesta: 135 0.042265 -0.027729 -0.004018
I wonder why it didnt complete Atomic Forces for Atom number:136-138!
A completed output is also attached, and pls note that I used PSP flles from Simune and
PAO information from the forum.
I hope Siesta users can suggest an indication in this error log.
nohup.zip (16.1 KB)
Thanks in advance
Krishna
INPUT
SystemName zif67optical
SystemLabel zif67optical
NumberOfSpecies 4
NumberOfAtoms 138
%block ChemicalSpeciesLabel
1 27 Co
2 7 N
3 6 C
4 1 H
%endblock ChemicalSpeciesLabel
PAO.BasisSize DZP
PAO.BasisType split
PAO.EnergyShift 0.02 Ry
XC.Functional GGA
XC.Authors PBE
kgrid.Cutoff 0. Bohr # Gamma only, didnt work (use this OR below one)
%block kgrid_Monkhorst_Pack
4 0 0 0.5
0 4 0 0.5
0 0 4 0.5
%endblock kgrid_Monkhorst_Pack
MinSCFIterations 3
MaxSCFIterations 1000
MeshCutoff 350 Ry
DM.MixingWeight 0.025
SCF.Mixer.History 6 # replace DM.NumberPulay
scf.Mixer.Variant GR
scf.Mixer.Kick 3
DM.Tolerance 0.001
XC.functional GGA
XC.authors PBE
SolutionMethod diagon
ElectronicTemperature 300 K
optical
OpticalCalculation .true.
%block Optical.Mesh
12 12 12
%endblock Optical.Mesh
Optical.OffsetMesh .true.
Optical.PolarizationType polarized
Optical.Scissor 0.45 eV
%block Optical.Vector
1.0 0.0 0.0
%endblock Optical.Vector
Optical.Broaden 0.2 eV
Optical.EnergyMaximum 20.0 eV # before it was 5 eV
Optical.EnergyMinimum 0.0 eV
dont use the below setting
#Optical.EnergyMaximum 3.12 eV
#Optical.EnergyMinimum 1.50 eV
%block PAO.Basis
Co 3 0.0
n=4 0 2 E 150.0 4.5
6.5 4.5
1.0 1.0
n=4 1 1 E 100.0 4.5
6.5
1.0
n=3 2 2 E 100.0 4.5
6.5 4.5
1.0 1.0
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
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 10 -0.7
10.0 5.0
n=1 1 1 E 10 -0.7 Q 2.0 1.0
10.0
%endblock PAO.Basis
step 0.00625 bohr
LatticeConstant 1 Ang
%block LatticeVectors
14.343458 0.226118 0.414646
-4.567967 13.577006 0.405857
-4.549189 -6.430382 11.941912
%endblock LatticeVectors
AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
0.24202465 0.76920472 0.50313464 1
0.76894173 0.24339087 0.50354967 1
0.50347176 0.24250779 0.76969774 1
0.50350372 0.76987367 0.24248714 1
0.76985359 0.50473562 0.24231154 1
0.24156771 0.50344063 0.76862835 1
0.36591256 0.90230097 0.61403896 2
0.27884029 0.73807263 0.37836213 2
0.70409660 0.08713014 0.43059503 2
0.66693367 0.25819042 0.56818661 2
0.61397867 0.36589156 0.90203288 2
0.38031718 0.28197305 0.73794270 2
0.43050814 0.70421504 0.08594667 2
0.57043369 0.66942834 0.25931384 2
0.90303357 0.61500080 0.36525068 2
0.73916914 0.38077451 0.28124399 2
0.08547264 0.42975643 0.70439298 2
0.25607635 0.56697154 0.66481255 2
0.90219219 0.36710907 0.61418066 2
0.73961502 0.28075750 0.37921019 2
0.08652751 0.70434607 0.43007596 2
0.25619205 0.66594723 0.56624626 2
0.36470863 0.61437072 0.90171113 2
0.28081409 0.38020659 0.73798204 2
0.70382489 0.43167989 0.08601353 2
0.66955253 0.57139822 0.25931121 2
0.61461063 0.90316610 0.36532278 2
0.37921989 0.73820294 0.28094943 2
0.43030084 0.08613552 0.70404739 2
0.56893792 0.25806139 0.66752707 2
0.37409596 -0.00175437 0.60386408 3
0.38286493 0.76654217 0.38441302 3
0.60430596 -0.00100557 0.37342899 3
0.64536949 0.22705329 0.64508349 3
0.60391709 0.37467697 -0.00193561 3
0.38475049 0.38562601 0.76694340 3
0.37265141 0.60419047 -0.00228568 3
0.64784094 0.64857581 0.22882745 3
-0.00143215 0.60435170 0.37352989 3
0.76830589 0.38492170 0.38491786 3
-0.00218198 0.37424027 0.60413104 3
0.22429934 0.64285591 0.64227208 3
0.32738619 0.00586516 0.49973617 3
0.48325746 0.80873099 0.48559562 3
0.50017612 0.00616544 0.32856536 3
0.69578364 0.16601605 0.69351183 3
0.49963228 0.33093951 0.00563667 3
0.48513868 0.48766593 0.81131946 3
0.32748335 0.49987206 0.00541090 3
0.69899204 0.69981448 0.16987292 3
0.00605174 0.50012495 0.32793598 3
0.81172454 0.48548513 0.48668657 3
0.00577150 0.32984001 0.49979725 3
0.16203910 0.69135648 0.69041721 3
0.42343228 0.93382443 0.72637046 3
0.20727447 0.68770120 0.26628750 3
0.78049524 0.04566319 0.46257877 3
0.59877831 0.30801288 0.53922226 3
0.72589923 0.42276985 0.93290271 3
0.26860287 0.20907734 0.68655012 3
0.46234945 0.78084294 0.04404284 3
0.53941004 0.59876854 0.30650780 3
0.93495212 0.72719177 0.42299663 3
0.68773332 0.26888800 0.20803196 3
0.04351433 0.46116772 0.78114596 3
0.30770808 0.53954944 0.59794266 3
0.93346702 0.42385612 0.72648710 3
0.68776496 0.20851370 0.26700038 3
0.04528052 0.78124132 0.46142249 3
0.30784099 0.59916495 0.53828290 3
0.42306228 0.72639781 0.93320254 3
0.20868700 0.26811057 0.68655214 3
0.78037936 0.46239729 0.04374238 3
0.59938124 0.53961175 0.30644347 3
0.72640155 0.93501603 0.42384027 3
0.26785573 0.68794514 0.20773365 3
0.46141474 0.04421502 0.78075393 3
0.53959898 0.30804622 0.59928176 3
0.77909209 0.22050084 0.76000930 4
0.48153889 0.51922808 0.74880930 4
0.24907842 0.48404662 1.01172397 4
0.02048726 0.48860786 0.25383141 4
0.74832334 0.48284962 0.51681484 4
0.99585221 0.24475163 0.47551131 4
0.21587972 0.77011327 0.76383018 4
0.47534210 0.24611314 0.99695490 4
0.77242466 0.77752538 0.22734614 4
0.48722617 0.01924276 0.25366180 4
0.49073342 0.73989873 0.50257451 4
0.24735572 1.00775135 0.48412812 4
0.31549242 0.93486133 0.43116776 4
0.48214184 0.86457031 0.55710490 4
0.49970245 0.07500632 0.38939199 4
0.55843508 0.47405394 0.83422349 4
0.64116488 0.71724175 0.11455434 4
0.92965980 0.43143683 0.30561714 4
0.83503770 0.55823947 0.47184946 4
0.07409567 0.49870641 0.38872273 4
0.31249783 0.43229108 0.93192161 4
0.72296685 0.64434756 0.12019335 4
0.43233799 0.93012084 0.30840754 4
0.55640380 0.85061245 0.47719146 4
0.64550924 0.12484949 0.72712671 4
0.38237238 0.08127123 0.50298694 4
0.50853587 0.38198204 0.08602527 4
0.49198766 0.55235684 0.88224995 4
0.88209331 0.49378685 0.55285375 4
0.94203591 0.33102013 0.43436009 4
0.10666811 0.70663563 0.63028088 4
0.08669481 0.37949397 0.50918193 4
0.11306360 0.63508910 0.71392151 4
0.38528273 0.50115138 0.07777809 4
0.43527604 0.33176031 0.94071987 4
0.70187411 0.10305387 0.63102654 4
0.42897173 0.87352672 0.75674936 4
0.11941684 0.65527384 0.23868144 4
0.86732275 0.09987164 0.51015536 4
0.59944124 0.33779144 0.47719427 4
0.75483788 0.42643360 0.87135924 4
0.24289786 0.12130706 0.65271091 4
0.50938502 0.86791200 0.09858254 4
0.47808165 0.59888504 0.33725236 4
0.87475786 0.75781713 0.42771103 4
0.65381049 0.24279549 0.12017410 4
0.09733384 0.50704456 0.86846556 4
0.33904368 0.47901968 0.60011735 4
0.87282868 0.42867931 0.75657282 4
0.65492035 0.12051658 0.23984150 4
0.09954601 0.86826622 0.50817317 4
0.33873606 0.60067087 0.47706117 4
0.42709015 0.75587879 0.87207402 4
0.12097388 0.24163163 0.65394212 4
0.86730648 0.50983446 0.09846904 4
0.60025638 0.47795147 0.33662401 4
0.75667947 0.87460940 0.42866203 4
0.24217565 0.65473456 0.11993758 4
0.50603827 0.09809385 0.86799991 4
0.47965853 0.34003918 0.60167170 4
%endblock AtomicCoordinatesAndAtomicSpecies
WriteCoorStep .true.
WriteForces .true.
WriteKpoints .false.
WriteCoorXmol .true.****strong text