Quickstart guide with example input file

A short example illustrating how to run the complete workflow, and obtain the shortest path to some of the products.

#!/bin/sh

# Reactions discovery example for a mixture of CH3CH2 and OH radicals
# The mixture should form ethanol CH3CH2OH and hydrogen peroxide HOOH
# and possibly more products.

rm -rf complete_nanoreactor.results

AMS_JOBNAME=complete_nanoreactor $AMSBIN/reactions_discovery << eor
   MolecularDynamics
      Enabled Yes
      NumSimulations 4
      BuildSystem
         NumAtoms 50
         Density 0.9
         Molecule 
            SMILES C[CH2]  # a CH3CH2 radical
            MoleFraction 1
         End
         Molecule 
            SMILES [OH]   # an OH radical
            MoleFraction 3
         End
      End
      Type NanoReactor
      NanoReactor
         NumCycles 5
         Temperature 500
         MinVolumeFraction 0.6
      End
      BondOrders Method=Guess
   End

   NetworkExtraction Enabled=Yes UseCharges=Yes
   ProductRanking Enabled=Yes

   Engine ReaxFF
      ForceField CHON-2019.ff
      TaperBO Yes
   EndEngine
eor

# Read and print the paths created for the first two stable products
export AMS_JOBNAME=reaction_paths
$AMSBIN/reactions_discovery << eor
    SearchNetwork
        Enabled Yes
        ReactionNetwork complete_nanoreactor.results
        ShortestPaths
            FirstNProducts 4
        End
    End
eor