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. <https://urldefense.com/v3/__https://forum.simuneatomistics.com/t/optical-spectrum-of-zeolite/3865*but-when-i-tried-the-calculation-pls-see-below-part-it-runs-and-completed-scf-cycle-and-it-seems-it-stuck-in-the-portion-1__;Iw!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEdoEwbtYg$ >But when I tried the calculation (Pls see below part) it runs and completed SCF cycle and it seems it stuck in the portion: -------------------------------------------------------------------- <https://urldefense.com/v3/__https://forum.simuneatomistics.com/t/optical-spectrum-of-zeolite/3865*h-130-0012952-0089863-0127418-131-0020422-0101546-0046036-132-0047941-0009764-0000107-133-0043814-0020094-0131299-134-0056622-0062521-0031526-135-0042265-0027729-0004018-136-0016008-0021773-0020389-137-0063636-0039750-0033829-138-0055053-0033202-0021522-2__;Iw!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEdlcDeZEg$ >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 <https://urldefense.com/v3/__https://forum.simuneatomistics.com/t/optical-spectrum-of-zeolite/3865*tot-0005242-0008209-0009872-3__;Iw!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEfYojfAHA$ >Tot -0.005242 0.008209 -0.009872 <https://urldefense.com/v3/__https://forum.simuneatomistics.com/t/optical-spectrum-of-zeolite/3865*max-0337362-res-0065680-sqrt-sum-f_i2-3n-4__;Iw!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEfqk6h3hw$ >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 <https://urldefense.com/v3/__https://forum.simuneatomistics.com/t/optical-spectrum-of-zeolite/3865*siesta-atomic-forces-evang-siesta-1-0026727-0000182-0015051-siesta-2-0044114-0043744-0001681-siesta-3-0020104-0007544-0115776-siesta-4-0054796-0053486-0025071-siesta-129-0036863-0041463-0047218-siesta-130-0012952-0089863-0127418-siesta-131-0020422-0101546-0046036-siesta-132-0047941-0009764-0000107-siesta-133-0043814-0020094-0131299-siesta-134-0056622-0062521-0031526-siesta-135-0042265-0027729-0004018-5__;Iw!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEf1TxHBVQ$ >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 <https://urldefense.com/v3/__https://forum.simuneatomistics.com/uploads/short-url/r6oNFu1wJasmVEKAdetIaKbnMgI.zip__;!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEd_od-aLA$ > (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 %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 <https://urldefense.com/v3/__https://forum.simuneatomistics.com/tag/scf__;!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEfSQ0QEeA$ >.Mixer.Variant GR scf <https://urldefense.com/v3/__https://forum.simuneatomistics.com/tag/scf__;!!D9dNQwwGXtA!SMMdFpD3A4w-sRoKBDli5IFKLO7pUv1jp2Jk1JyRjy_og5_ZUXrAjQYZg2TrQlfV9ti9CXn4RjAtLpwgZEfSQ0QEeA$ >.Mixer.Kick 3 DM.Tolerance 0.001 XC.functional GGA XC.authors PBE SolutionMethod diagon ElectronicTemperature 300 K OpticalCalculation .true. %block Optical.Mesh 12 12 12 %endblock Optical.Mesh Optical.OffsetMesh .true. Optical.PolarizationType polarized %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 %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 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 -- **--------------------------------------------------------------------------------------------------------------** **Go Green: DO NOT print this e-mail unless absolutely necessary. Save paper, Save Trees.** *--- *Disclaimer* ---* *The information in this mail, including any attachments, is confidential and is intended solely for the addressee. Access to this mail by anyone else is unauthorized. Copying or further distribution beyond the original recipient may be unlawful if you are not the intended recipient. Please contact the sender by reply email and destroy all copies of the original message. Any opinion expressed in this mail is that of the sender and does not necessarily reflect that of *Mar Baselios College of Engineering and Technology*, Thiruvananthapuram.*
<<attachment: nohup.zip>>
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