# Mode tracking vs full normal modes for dydrogesterone Method: ADF/PBE/DZ with large frozen core. Dydrogesterone was constructed from the requested SMILES. ChemicalSystem bond orders and ring membership identified the non-ring C=O as C2–O3 (1-based), assigned to region `CO`. ## Mode displacement image ![mode displacement](mode_displacement_grid.png) ## IR spectra ![partial](partial_hessian_spectrum.png) ![mode tracking](mode_tracking_spectrum.png) ![full](full_spectrum.png) ## Selected C=O mode | calculation | mode | frequency_cm-1 | intensity_km/mol | CO_displacement_fraction | |:---------------------------------|-------:|-----------------:|-------------------:|---------------------------:| | Partial Hessian guess | 153 | 1533.738 | 115.744 | 1.000 | | Mode tracking | 1 | 1562.423 | 86.508 | 0.374 | | Full normal modes (best overlap) | 117 | 1560.353 | 83.544 | 0.350 | ## Timings | job | description | wall_s | |:----------------------|:----------------------------|---------:| | 01_opt | Geometry optimization | 348.0 | | 02_partial_hessian | CO-region partial Hessian | 131.0 | | 03_mode_tracking | Mode tracking from mode 153 | 440.0 | | 04_full_normal_modes | Full normal modes | 1803.0 | | partial+mode_tracking | Selective workflow | 571.0 | Selective partial-Hessian + mode-tracking time = 571.0 s vs full normal modes = 1803.0 s, speedup = 3.16x. ## Conclusion Mode tracking gives a C=O frequency and intensity very close to the corresponding full normal-mode result, while requiring much less wall time than the full Hessian. ## Provenance and inputs ### opt: `01-run_workdir/01_opt` Geometry optimization at ADF/PBE/DZ large core. ```ams Task GeometryOptimization System Atoms C -4.5753007624 2.4335757077 -0.3051238140 C -4.1654044269 1.4231319749 0.7300567028 region=CO O -4.4674968841 1.6330354323 1.8950202972 region=CO C -3.4249194595 0.1349544347 0.3858899036 C -3.3192691179 -0.1859566386 -1.1125546573 C -2.0693702052 -1.0486415561 -1.2804430380 C -1.3924473893 -1.1266345242 0.0973200504 C -1.9726158255 0.0491246723 0.9254402220 C -1.1997086852 1.3730512519 0.6537656577 C 0.3222386059 1.2194765553 0.7371377451 C 0.8338420837 0.1739848117 -0.2850518607 C 0.1597751178 -1.1965994917 0.0065967194 C 0.7603192912 -1.8095625610 1.2512107198 C 2.0788335458 -1.8018448697 1.4263619842 C 2.9391408645 -1.1699416326 0.4132904296 C 4.1328084585 -1.7217137353 0.1453610078 C 4.9015536137 -1.3363797622 -1.0501572441 O 6.0660755057 -1.7889615227 -1.2081132259 C 4.3173352277 -0.4223716682 -2.0919404215 C 2.8083777155 -0.1913471249 -1.8811425169 C 2.4223452480 0.0318179121 -0.3877414796 C 3.1524503365 1.2995573959 0.1344050991 C -1.9750236367 -0.2703983542 2.4407161276 H -5.2374058363 1.9570953870 -1.0578338512 H -3.6770724868 2.8518506737 -0.8043078900 H -5.1308577997 3.2722925799 0.1664734311 H -4.0167277510 -0.6968517270 0.8346116809 H -3.1923349535 0.7292849107 -1.7274037391 H -4.2265497822 -0.7238688541 -1.4649990443 H -1.4024495612 -0.5921318180 -2.0431039754 H -2.3440017427 -2.0668804766 -1.6343452623 H -1.7508120077 -2.0825689555 0.5474413253 H -1.4447604627 1.7617058398 -0.3585794330 H -1.5182697896 2.1543818490 1.3782845605 H 0.7454608423 2.2195687215 0.5081281572 H 0.6300684955 0.9484578987 1.7688376311 H 0.4645801947 0.5269992359 -1.2733759104 H 0.4129277678 -1.8847911774 -0.8310984850 H 0.1367904154 -2.3082919568 1.9827164786 H 2.5127169465 -2.3283090113 2.2680463583 H 4.4996337377 -2.5454953282 0.7474026720 H 4.8575609769 0.5477101379 -2.0691281882 H 4.4765118113 -0.8661087541 -3.0983229054 H 2.4950166965 0.6819829426 -2.4946876398 H 2.2624511353 -1.0792067427 -2.2710233174 H 2.8637673384 2.1918824411 -0.4610878495 H 4.2554742135 1.1973245897 0.0771896657 H 2.9244125570 1.4787509336 1.2061068447 H -2.4612486216 0.5441744889 3.0152424596 H -2.5221771041 -1.2147790409 2.6483217466 H -0.9462444517 -0.3755354951 2.8356480095 End BondOrders 1 2 1.0 1 24 1.0 1 25 1.0 1 26 1.0 2 3 2.0 2 4 1.0 4 5 1.0 4 8 1.0 4 27 1.0 5 6 1.0 5 28 1.0 5 29 1.0 6 7 1.0 6 30 1.0 6 31 1.0 7 8 1.0 7 12 1.0 7 32 1.0 8 9 1.0 8 23 1.0 9 10 1.0 9 33 1.0 9 34 1.0 10 11 1.0 10 35 1.0 10 36 1.0 11 12 1.0 11 21 1.0 11 37 1.0 12 13 1.0 12 38 1.0 13 14 2.0 13 39 1.0 14 15 1.0 14 40 1.0 15 16 2.0 15 21 1.0 16 17 1.0 16 41 1.0 17 18 2.0 17 19 1.0 19 20 1.0 19 42 1.0 19 43 1.0 20 21 1.0 20 44 1.0 20 45 1.0 21 22 1.0 22 46 1.0 22 47 1.0 22 48 1.0 23 49 1.0 23 50 1.0 23 51 1.0 End End Engine adf Basis Core Large Type DZ End XC GGA PBE End EndEngine ``` ### partial: `02-continue_workdir/02_partial_hessian` Partial Hessian / normal-modes calculation restricted to CO region. ```ams NormalModes ReScanModes no End Properties NormalModes yes SelectedRegionForHessian CO End Task SinglePoint System Atoms C -4.5319269049 2.4489057819 -0.1266719978 C -4.2469227153 1.3078809949 0.8293588846 region=CO O -4.6530787271 1.3640220185 2.0211398418 region=CO C -3.4689421686 0.0871517694 0.3591813709 C -3.3585772471 -0.1547569368 -1.1697998017 C -2.0459432386 -0.9813621909 -1.3681096305 C -1.3992200107 -1.1200174701 0.0439506404 C -1.9784921099 0.0574928560 0.8902091955 C -1.2300829648 1.3695706616 0.5459659072 C 0.3051208599 1.2291440267 0.6600470278 C 0.8302861210 0.1558311317 -0.3226725508 C 0.1467191411 -1.2086947645 0.0073548278 C 0.7388901329 -1.7620123046 1.2889587699 C 2.0771909169 -1.7194374740 1.4858758488 C 2.9298387032 -1.1680053509 0.4350207664 C 4.1519376618 -1.7186909523 0.1660898354 C 4.9552240909 -1.3641843554 -1.0035185199 O 6.1256772709 -1.8284561992 -1.1647532365 C 4.3313411414 -0.4529542293 -2.0565709976 C 2.8096419197 -0.2606947107 -1.8856430283 C 2.4046272791 0.0084815730 -0.4051833549 C 3.1293007137 1.2865649385 0.1099535243 C -1.9498023112 -0.2043487418 2.4083021698 H -5.2188794642 2.1118323938 -0.9232765188 H -3.6132827008 2.8181311167 -0.6105309970 H -5.0082179145 3.2629770567 0.4381364126 H -3.9665551327 -0.7814731795 0.8312939829 H -3.2952089715 0.7962816324 -1.7210196277 H -4.2455540736 -0.6911111993 -1.5458737279 H -1.3650826442 -0.4633739864 -2.0636550793 H -2.2514975769 -1.9767098151 -1.7962965378 H -1.7762925426 -2.0582910184 0.4970591002 H -1.4669009115 1.6769839874 -0.4901591001 H -1.5794507713 2.1759705462 1.2180498752 H 0.7560293390 2.2084591953 0.4308065219 H 0.5910114310 0.9709612485 1.6941792179 H 0.5020584773 0.4646152353 -1.3339354749 H 0.4057189942 -1.9276512436 -0.8008994923 H 0.0860043289 -2.2654120124 2.0082370760 H 2.5449642773 -2.1989762673 2.3515551787 H 4.5593710931 -2.5149786849 0.7963210784 H 4.8598133002 0.5169670446 -2.0155853495 H 4.5674579675 -0.8896962719 -3.0423644307 H 2.4654295464 0.5789179285 -2.5161414977 H 2.2905085734 -1.1760185463 -2.2255074669 H 2.8407409696 2.1669200764 -0.4893639455 H 4.2209215079 1.1604766950 0.0468392050 H 2.8856457942 1.4765735719 1.1669734994 H -2.5554393950 0.5508254965 2.9367517979 H -2.3828888284 -1.1933890656 2.6391530348 H -0.9232322273 -0.1712420059 2.8062257114 End BondOrders 1 2 1.0 1 24 1.0 1 25 1.0 1 26 1.0 2 3 2.0 2 4 1.0 4 5 1.0 4 8 1.0 4 27 1.0 5 6 1.0 5 28 1.0 5 29 1.0 6 7 1.0 6 30 1.0 6 31 1.0 7 8 1.0 7 12 1.0 7 32 1.0 8 9 1.0 8 23 1.0 9 10 1.0 9 33 1.0 9 34 1.0 10 11 1.0 10 35 1.0 10 36 1.0 11 12 1.0 11 21 1.0 11 37 1.0 12 13 1.0 12 38 1.0 13 14 2.0 13 39 1.0 14 15 1.0 14 40 1.0 15 16 2.0 15 21 1.0 16 17 1.0 16 41 1.0 17 18 2.0 17 19 1.0 19 20 1.0 19 42 1.0 19 43 1.0 20 21 1.0 20 44 1.0 20 45 1.0 21 22 1.0 22 46 1.0 22 47 1.0 22 48 1.0 23 49 1.0 23 50 1.0 23 51 1.0 End End Engine adf Basis Core Large Type DZ End XC GGA PBE End EndEngine ``` ### mt: `03-rest_workdir/03_mode_tracking` Mode tracking started from partial-Hessian C=O stretch mode 153. ```ams Task VibrationalAnalysis VibrationalAnalysis ModeTracking HessianGuess File HessianPath /home/ubuntu/work/02-continue_workdir/02_partial_hessian/adf.rkf TrackingMethod OverlapPrevious End NormalModes ModeFile /home/ubuntu/work/02-continue_workdir/02_partial_hessian/adf.rkf ModeInputFormat File ModeSelect ModeNumber 153 End End Type ModeTracking End System Atoms C -4.5319269049 2.4489057819 -0.1266719978 C -4.2469227153 1.3078809949 0.8293588846 region=CO O -4.6530787271 1.3640220185 2.0211398418 region=CO C -3.4689421686 0.0871517694 0.3591813709 C -3.3585772471 -0.1547569368 -1.1697998017 C -2.0459432386 -0.9813621909 -1.3681096305 C -1.3992200107 -1.1200174701 0.0439506404 C -1.9784921099 0.0574928560 0.8902091955 C -1.2300829648 1.3695706616 0.5459659072 C 0.3051208599 1.2291440267 0.6600470278 C 0.8302861210 0.1558311317 -0.3226725508 C 0.1467191411 -1.2086947645 0.0073548278 C 0.7388901329 -1.7620123046 1.2889587699 C 2.0771909169 -1.7194374740 1.4858758488 C 2.9298387032 -1.1680053509 0.4350207664 C 4.1519376618 -1.7186909523 0.1660898354 C 4.9552240909 -1.3641843554 -1.0035185199 O 6.1256772709 -1.8284561992 -1.1647532365 C 4.3313411414 -0.4529542293 -2.0565709976 C 2.8096419197 -0.2606947107 -1.8856430283 C 2.4046272791 0.0084815730 -0.4051833549 C 3.1293007137 1.2865649385 0.1099535243 C -1.9498023112 -0.2043487418 2.4083021698 H -5.2188794642 2.1118323938 -0.9232765188 H -3.6132827008 2.8181311167 -0.6105309970 H -5.0082179145 3.2629770567 0.4381364126 H -3.9665551327 -0.7814731795 0.8312939829 H -3.2952089715 0.7962816324 -1.7210196277 H -4.2455540736 -0.6911111993 -1.5458737279 H -1.3650826442 -0.4633739864 -2.0636550793 H -2.2514975769 -1.9767098151 -1.7962965378 H -1.7762925426 -2.0582910184 0.4970591002 H -1.4669009115 1.6769839874 -0.4901591001 H -1.5794507713 2.1759705462 1.2180498752 H 0.7560293390 2.2084591953 0.4308065219 H 0.5910114310 0.9709612485 1.6941792179 H 0.5020584773 0.4646152353 -1.3339354749 H 0.4057189942 -1.9276512436 -0.8008994923 H 0.0860043289 -2.2654120124 2.0082370760 H 2.5449642773 -2.1989762673 2.3515551787 H 4.5593710931 -2.5149786849 0.7963210784 H 4.8598133002 0.5169670446 -2.0155853495 H 4.5674579675 -0.8896962719 -3.0423644307 H 2.4654295464 0.5789179285 -2.5161414977 H 2.2905085734 -1.1760185463 -2.2255074669 H 2.8407409696 2.1669200764 -0.4893639455 H 4.2209215079 1.1604766950 0.0468392050 H 2.8856457942 1.4765735719 1.1669734994 H -2.5554393950 0.5508254965 2.9367517979 H -2.3828888284 -1.1933890656 2.6391530348 H -0.9232322273 -0.1712420059 2.8062257114 End BondOrders 1 2 1.0 1 24 1.0 1 25 1.0 1 26 1.0 2 3 2.0 2 4 1.0 4 5 1.0 4 8 1.0 4 27 1.0 5 6 1.0 5 28 1.0 5 29 1.0 6 7 1.0 6 30 1.0 6 31 1.0 7 8 1.0 7 12 1.0 7 32 1.0 8 9 1.0 8 23 1.0 9 10 1.0 9 33 1.0 9 34 1.0 10 11 1.0 10 35 1.0 10 36 1.0 11 12 1.0 11 21 1.0 11 37 1.0 12 13 1.0 12 38 1.0 13 14 2.0 13 39 1.0 14 15 1.0 14 40 1.0 15 16 2.0 15 21 1.0 16 17 1.0 16 41 1.0 17 18 2.0 17 19 1.0 19 20 1.0 19 42 1.0 19 43 1.0 20 21 1.0 20 44 1.0 20 45 1.0 21 22 1.0 22 46 1.0 22 47 1.0 22 48 1.0 23 49 1.0 23 50 1.0 23 51 1.0 End End Engine adf Basis Core Large Type DZ End XC GGA PBE End EndEngine ``` ### full: `03-rest_workdir/04_full_normal_modes` Full normal-modes verification calculation. ```ams NormalModes ReScanModes no End Properties NormalModes yes End Task SinglePoint System Atoms C -4.5319269049 2.4489057819 -0.1266719978 C -4.2469227153 1.3078809949 0.8293588846 region=CO O -4.6530787271 1.3640220185 2.0211398418 region=CO C -3.4689421686 0.0871517694 0.3591813709 C -3.3585772471 -0.1547569368 -1.1697998017 C -2.0459432386 -0.9813621909 -1.3681096305 C -1.3992200107 -1.1200174701 0.0439506404 C -1.9784921099 0.0574928560 0.8902091955 C -1.2300829648 1.3695706616 0.5459659072 C 0.3051208599 1.2291440267 0.6600470278 C 0.8302861210 0.1558311317 -0.3226725508 C 0.1467191411 -1.2086947645 0.0073548278 C 0.7388901329 -1.7620123046 1.2889587699 C 2.0771909169 -1.7194374740 1.4858758488 C 2.9298387032 -1.1680053509 0.4350207664 C 4.1519376618 -1.7186909523 0.1660898354 C 4.9552240909 -1.3641843554 -1.0035185199 O 6.1256772709 -1.8284561992 -1.1647532365 C 4.3313411414 -0.4529542293 -2.0565709976 C 2.8096419197 -0.2606947107 -1.8856430283 C 2.4046272791 0.0084815730 -0.4051833549 C 3.1293007137 1.2865649385 0.1099535243 C -1.9498023112 -0.2043487418 2.4083021698 H -5.2188794642 2.1118323938 -0.9232765188 H -3.6132827008 2.8181311167 -0.6105309970 H -5.0082179145 3.2629770567 0.4381364126 H -3.9665551327 -0.7814731795 0.8312939829 H -3.2952089715 0.7962816324 -1.7210196277 H -4.2455540736 -0.6911111993 -1.5458737279 H -1.3650826442 -0.4633739864 -2.0636550793 H -2.2514975769 -1.9767098151 -1.7962965378 H -1.7762925426 -2.0582910184 0.4970591002 H -1.4669009115 1.6769839874 -0.4901591001 H -1.5794507713 2.1759705462 1.2180498752 H 0.7560293390 2.2084591953 0.4308065219 H 0.5910114310 0.9709612485 1.6941792179 H 0.5020584773 0.4646152353 -1.3339354749 H 0.4057189942 -1.9276512436 -0.8008994923 H 0.0860043289 -2.2654120124 2.0082370760 H 2.5449642773 -2.1989762673 2.3515551787 H 4.5593710931 -2.5149786849 0.7963210784 H 4.8598133002 0.5169670446 -2.0155853495 H 4.5674579675 -0.8896962719 -3.0423644307 H 2.4654295464 0.5789179285 -2.5161414977 H 2.2905085734 -1.1760185463 -2.2255074669 H 2.8407409696 2.1669200764 -0.4893639455 H 4.2209215079 1.1604766950 0.0468392050 H 2.8856457942 1.4765735719 1.1669734994 H -2.5554393950 0.5508254965 2.9367517979 H -2.3828888284 -1.1933890656 2.6391530348 H -0.9232322273 -0.1712420059 2.8062257114 End BondOrders 1 2 1.0 1 24 1.0 1 25 1.0 1 26 1.0 2 3 2.0 2 4 1.0 4 5 1.0 4 8 1.0 4 27 1.0 5 6 1.0 5 28 1.0 5 29 1.0 6 7 1.0 6 30 1.0 6 31 1.0 7 8 1.0 7 12 1.0 7 32 1.0 8 9 1.0 8 23 1.0 9 10 1.0 9 33 1.0 9 34 1.0 10 11 1.0 10 35 1.0 10 36 1.0 11 12 1.0 11 21 1.0 11 37 1.0 12 13 1.0 12 38 1.0 13 14 2.0 13 39 1.0 14 15 1.0 14 40 1.0 15 16 2.0 15 21 1.0 16 17 1.0 16 41 1.0 17 18 2.0 17 19 1.0 19 20 1.0 19 42 1.0 19 43 1.0 20 21 1.0 20 44 1.0 20 45 1.0 21 22 1.0 22 46 1.0 22 47 1.0 22 48 1.0 23 49 1.0 23 50 1.0 23 51 1.0 End End Engine adf Basis Core Large Type DZ End XC GGA PBE End EndEngine ```