Example: Mode Refinement¶

#! /bin/sh

# This example shows a mode refinement of the band associated with the
# C=O and C=C stretch modes in the dydrogesterone molecule. This was one
# of the example calculations in the original paper on mode refinement:
#
#    J. Phys. Chem. Lett., 2018, 9 (23), pp 6878-6882


# Step 1: Get DFTB modes at the optimized DFT geometry
# ----------------------------------------------------

AMS_JOBNAME=FREQ_DFTB $ADFBIN/ams << EOF

   System
      Atoms
         # Dydrogesterone geometry already optimized with DFT (BP86/TZP).
         C 0.179402320119871 1.1462568499773749 -1.34045805553897
         C -1.0397129548582973 1.4038864822738149 -0.42742864655449175
         C -1.9187723039939633 0.15407663507305838 -0.2887082902723144
         C 5.26339021966562 -0.0803229279006518 0.15901574737297627
         C 4.387948120190181 -1.2500901532169464 0.1985138671042922
         C 3.0305058270434313 -1.2006020082109579 0.06687676611264043
         C 2.2733069275281843 0.12162323554336309 -0.08656132560038762
         C 3.224495049036027 1.1562588842598234 -0.7427294996476081
         C 4.589580248129175 1.2673670000240371 -0.055599205726051454
         C -2.593712600512111 -0.1967276203097069 -1.6287069723510241
         C -2.011183672049868 -2.0904848406306247 0.6637924766824627
         C -3.24333170765593 -1.3040476226855777 1.1949612943873085
         C -2.9910039148987044 0.19289628304945772 0.8647395097635705
         C 1.8832501895313913 0.6066618903839885 1.3319251022509289
         C -1.021215985785471 -0.9883577256376227 0.2595406535945511
         C 0.950572917185341 -2.499497885394989 -0.17845795742396
         C 2.2618422613458535 -2.429295894019406 0.12998062227671012
         C 0.14931427176016024 -1.3398555308999998 -0.6810919840203331
         C 1.0424571714734645 -0.11148243146945544 -1.0381151732514977
         C -4.261014768367461 0.9709543041281233 0.5302962418813911
         C -4.2770282131623745 2.4457823410117943 0.8829249061723259
         O -5.23153866013212 0.4348316478674291 0.006835058476534351
         O 6.486629619384615 -0.1787206146841789 0.3101830744372818
         H 4.496419281348679 1.7413060958817603 0.9361407723186962
         H 4.889108126023183 -2.2103967123783246 0.34783394165927906
         H -2.5053803890738937 0.6948315694295174 1.7185731459759712
         H 2.747947397670055 2.147017249296297 -0.7608107343500633
         H 3.3788188981072294 0.8618896159833123 -1.7937886227370627
         H 5.278515387629924 1.9033945262275014 -0.6280820487414189
         H -0.313881863508176 -1.6818474813482587 -1.6263008186833716
         H 2.7970964757389787 -3.3338033858599037 0.4312075853898926
         H 0.4355882565839679 -3.460258453470549 -0.09628540747796212
         H 2.7788926695047853 0.7904363143118734 1.939504792825026
         H 1.3142558486724543 1.5445870277271823 1.281760102768146
         H 1.2817550339094792 -0.13839730232383732 1.865618408504196
         H 1.519857325493626 -0.37989780969443004 -1.9963570252289853
         H -3.35526145791249 2.9466219355670638 0.5538746959825623
         H -0.5844412872674496 -0.5966200898063014 1.193600037988863
         H 0.8128688006525261 2.043605920072621 -1.3496094336049678
         H -0.18858319204633375 1.0503960522723468 -2.3730012879550473
         H -1.6112343483079186 2.2461900431605373 -0.8495116990527544
         H -0.710640496667605 1.7174589936204205 0.5760379282354502
         H -1.5937002785491352 -2.7672883134736264 1.4205298630102559
         H -2.2836000112559893 -2.709635208733019 -0.2046201598348845
         H -3.3761548431942434 -1.4386051747789588 2.276540650869438
         H -4.174084527825135 -1.628156544022731 0.7132317870749941
         H -1.860827847389362 -0.4325042173503644 -2.4102132115597854
         H -3.2757258446436426 -1.0505046678063983 -1.5382984747892279
         H -3.1932088604642455 0.6502553019056425 -1.9892714020438331
         H -4.314908973244162 2.55066722711135 1.9790476680048945
         H -5.155478941054673 2.9311753898910595 0.44480850527661253
      End
   End

   Task SinglePoint

   Properties
       NormalModes Yes
   End

   Engine DFTB
       Model DFTB3
       ResourcesDir DFTB.org/3ob-freq-1-2
   EndEngine

   # Do displacements for the numerical Hessian in parallel.
   NumericalDifferentiation
      Parallel nCoresPerGroup=1
   End

EOF


# Step 2: Mode refinement of the DFTB C=O and C=C stretch bands at the DFT level
# ------------------------------------------------------------------------------

AMS_JOBNAME=ModeRefinement $ADFBIN/ams << EOF

   LoadSystem
      File FREQ_DFTB.results/dftb.rkf
   End

   Task ModeRefinement

   ModeRefinement
      ModePath FREQ_DFTB.results/dftb.rkf
      ModeSelect
         FreqRange 1500 1800
      End
   End

   Engine BAND
      # Settings from the paper:
      XC
         GGA BP86
      End
      Basis
         Type TZP
      End
      # Just to make this test run faster:
      NumericalQuality Basic
   EndEngine

   NumericalDifferentiation
      # Do +/- displacements along the mode in parallel.
      Parallel nCoresPerGroup=1
   End

EOF