#!/bin/sh



echo "================="
echo "HCN isomerization"
echo "================="
echo

AMS_JOBNAME=HCN_isomerization $ADFBIN/ams << EOF

   Task PESScan
   # (Linear transit is just a PES scan with 1 scan coordinate.)

   System
      Atoms
         C       0.00000000       0.00000000       1.04219000
         H       0.00000000       0.00000000      -0.03324000
         N       0.00000000       0.00000000       2.20064000
      End
   End

   PESScan
      ScanCoordinate
         nPoints 25
         Angle  2 1 3  180.0 0.0
      End
   End

   Engine DFTB
      Model DFTB0
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF



echo
echo "==================="
echo "Water angle transit"
echo "==================="
echo

AMS_JOBNAME=water_angle $ADFBIN/ams << EOF

   Task PESScan

   System
      Atoms
         O       0.00000000       0.00000000       0.59372000
         H       0.00000000       0.76544000      -0.00836000
         H       0.00000000      -0.76544000      -0.00836000
      End
   End

   PESScan
      ScanCoordinate
         nPoints 25
         Angle  2 1 3  80.0 180.0
      End
   End

   GeometryOptimization
      ! Delocalized coordinates currently have a problem with linear systems.
      ! So we will use cartesian coordinates here.
      CoordinateType Cartesian
   End

   Engine DFTB
      Model DFTB0
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF



echo
echo "===================="
echo "Hydrocarbon reaction"
echo "===================="
echo

AMS_JOBNAME=hydcarb $ADFBIN/ams << EOF

   Task PESScan

   System
      Atoms
         C       0.14667300      -0.21503500       0.40053800
         C       1.45297400      -0.07836900       0.12424400
         C       2.23119700       1.15868100       0.12912100
         C       1.78331500       2.39701500       0.38779700
         H      -0.48348000       0.63110600       0.67664100
         H      -0.33261900      -1.19332100       0.35411600
         H       2.01546300      -0.97840100      -0.14506700
         H       3.29046200       1.03872500      -0.12139700
         H       2.45728900       3.25301000       0.35150400
         H       0.74193400       2.60120700       0.64028800
         C      -0.75086900       1.37782400      -2.43303700
         C      -0.05392100       2.51281000      -2.41769100
         H      -1.78964800       1.33942600      -2.09651100
         H      -0.30849400       0.43896500      -2.76734700
         H      -0.49177100       3.45043100      -2.06789100
         H       0.98633900       2.54913500      -2.74329400
      End
   End

   PESScan
      ScanCoordinate
         nPoints 25
         Distance  1 11   3.36  1.538
         Distance  4 12   3.36  1.538
      End
   End

   Engine DFTB
      Model DFTB0
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF



echo
echo "====================================="
echo "Retinal trans -> 11-cis isomerization"
echo "====================================="
echo

AMS_JOBNAME=retinal_transcis $ADFBIN/ams << EOF

   Task PESScan

   System
      Atoms
         H      -2.10968473      -1.58238733       0.78224517
         C      -2.10306857      -0.54058322       0.46363503
         C      -0.89436995       0.04807217       0.25528247
         H      -0.85555481       1.05432693      -0.15803658
         C       0.38987539      -0.58661182       0.49038464
         C       1.53213446       0.09657801       0.14394773
         H       1.40518949       1.08783970      -0.29205231
         H       3.05232192      -1.34477492       0.72115301
         C       2.88311454      -0.36358433       0.28105432
         C       3.96024700       0.37378345      -0.12385974
         H       3.77965758       1.35231793      -0.56821856
         C       5.34627719      -0.04025647      -0.02249097
         C       6.32191717       0.80135945      -0.49190463
         H       6.00090638       1.74979100      -0.92101391
         C      -4.46825064      -0.90426552      -0.39585925
         C      -5.87277429      -0.25303564      -0.45007491
         C      -3.41139545       0.06493448       0.19516310
         C      -3.67932839       1.38221399       0.41656971
         C      -5.81598497       1.19032366      -0.92660753
         C      -5.00049358       2.01922634       0.05561242
         C      -4.58391145      -2.18782901       0.46346394
         C      -4.01729542      -1.30039402      -1.82272212
         C      -2.72429960       2.32303313       1.10290124
         C       0.40919453      -1.96244629       1.09501374
         C       5.64155973      -1.38034133       0.59419110
         C       7.76996060       0.56699126      -0.48750226
         O       8.57693167       1.36615612      -0.92976322
         H      -6.51997817      -0.84904979      -1.10100203
         H      -6.32039371      -0.28079023       0.54871092
         H      -5.36159995       1.23817633      -1.92112092
         H      -6.82595442       1.60207678      -1.01946858
         H      -5.58216571       2.18390764       0.97424181
         H      -4.81292271       3.01993001      -0.35246294
         H      -4.74166770      -1.94289144       1.51126095
         H      -5.43008715      -2.78247632       0.12572479
         H      -3.69644845      -2.81116549       0.38705593
         H      -3.02900804      -1.75403268      -1.79820003
         H      -4.71056940      -2.01489741      -2.26202914
         H      -3.97070839      -0.42860260      -2.47090348
         H      -2.16469005       2.92261100       0.38111736
         H      -3.27791517       3.02297911       1.72885233
         H      -2.00470188       1.79865198       1.72726573
         H      -0.13689001      -1.97717074       2.03825359
         H      -0.07664772      -2.68134154       0.43362393
         H       1.41837401      -2.31391556       1.28591185
         H       5.15278730      -2.17622743       0.03222328
         H       6.70436647      -1.59729505       0.62729622
         H       5.25700064      -1.42489613       1.61313095
         H       8.12614442      -0.41441814      -0.04549414
      End
   End

   PESScan
      ScanCoordinate
         nPoints 25
         Dihedral  6 9 10 12  180  0
         Dihedral  8 9 10 11  180  0
      End
   End

   Engine DFTB
      Model DFTB0
      ResourcesDir DFTB.org/mio-1-1
   EndEngine

EOF