Example: Importing conformers into PES explorations
***************************************************

"Download import_into_pesexp.run"

   #!/bin/sh


   # Step 1: Run the conformer tool to quickly get a set of minima on the PES
   # ------------------------------------------------------------------------

   $AMSBIN/conformers << EOF

   Generator
      RDKit
         InitialNConformers 100
      End
   End

   System
       Atoms
           N -1.912873733399416 2.022897940092991 -0.1378294583620503
           C -0.871664156578182 3.02960778940094 0.06584379364356192
           C 0.5013812000791015 2.352115382193892 0.0410146984615521
           O 0.812167345172201 1.847076794564962 -1.240836870209463
           H -1.850257440384896 1.675835972092315 -1.088966428216949
           H -2.82010628990089 2.459772455658122 -0.02412199180453132
           H -1.024866752021569 3.492408399687411 1.045420209976512
           H -0.9134720948542179 3.809309747393572 -0.7093004343600406
           H 0.5270488401868264 1.547182041972351 0.7934160458635944
           H 1.275876827761384 3.088526288396493 0.2854207086154862
           H 0.2041922851100986 1.132993293447435 -1.463777763138591
       End
       BondOrders
            1 2 1.0
            1 5 1.0
            1 6 1.0
            2 3 1.0
            2 7 1.0
            2 8 1.0
            3 4 1.0
            3 9 1.0
            3 10 1.0
            4 11 1.0
       End
   End

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

   RNGSeed 20200512 # Just to make the test output deterministic ...

   EOF


   # Step 2: Import energy landscape by running a LandscapeRefinement on it
   # ----------------------------------------------------------------------
   #
   # The energy landscape that is produced by the conformers tool does not contain
   # the engine output files of the individual states, which contain e.g. the
   # normal modes. It can be used as input to the PESExploration ->
   # LandscapeRefinement job, but not for the other PESExploration jobs (e.g.
   # ProcessSearch). You should therefore always run the conformers output through
   # a quick LandscapeRefinement before proceeding to other PES exploration jobs.
   #
   # At this point you can also trim down the number of minima loaded from the set
   # of conformers. In the example below, we only load the 10 lowest energy
   # conformers.


   AMS_JOBNAME=refinement $AMSBIN/ams << EOF

   Task PESExploration

   PESExploration
      Job LandscapeRefinement
      LoadEnergyLandscape
        Path conformers.results/conformers.rkf
        KeepOnly 1:10
      End
   End

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

   RNGSeed 20200512 # Just to make the test output deterministic ...

   EOF


   # Step 3: Run a process search around the lowest energy conformer
   # ---------------------------------------------------------------
   #
   # We load all states we got from the LandscapeRefinement and run a single
   # expedition around the lowest energy conformer. This will give us a set of
   # transition states connecting it to other conformers, but possibly also other
   # isomers.


   AMS_JOBNAME=process_search $AMSBIN/ams << EOF

   Task PESExploration

   PESExploration
      Job ProcessSearch
      LoadEnergyLandscape
        Path refinement.results
        SeedStates 1
      End
      DynamicSeedStates False
      NumExpeditions 1
      NumExplorers 64
   End

   LoadSystem
      File refinement.results/ams.rkf
   End

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

   RNGSeed 20200512 # Just to make the test output deterministic ...

   EOF

   # Note that DFTB0 wrongly predicts an energetically favorable proton transfer
   # from the OH group to the NH2 group. This would not have happened if we had
   # used SCC-DFTB, but it is a nice example to show off the input for these jobs
   # and that the PES exploration can discover also isomers, while the conformer
   # tool should only produce conformers.
