Quickstart guide with example input file
****************************************

A short example illustrating how to run the complete workflow, and how
to restart from previous calculations.

   #!/bin/sh

   # Reactions discovery example for a mixutre 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

   #Test if ethanol is found:
   echo ETHANOL: `grep -c " CCO " complete_nanoreactor.results/reactions_discovery.log`
   #Test if hydrogen peroxide is found:
   echo HYDROGEN PEROXIDE: `grep -c " OO " complete_nanoreactor.results/reactions_discovery.log`

   # Use the MD trajectories from the previous job
   rm -rf restart_extraction.results
   AMS_JOBNAME=restart_extraction $AMSBIN/reactions_discovery << eor
       MolecularDynamics Enabled=No
       NetworkExtraction Enabled=Yes MDTrajectories=complete_nanoreactor.results
       ProductRanking Enabled=Yes
       Engine ReaxFF
           ForceField CHON-2019.ff
           TaperBO Yes
       EndEngine
   eor

   #Test if ethanol is found:
   echo ETHANOL: `grep -c " CCO " restart_extraction.results/reactions_discovery.log`
   #Test if hydrogen peroxide is found:
   echo HYDROGEN PEROXIDE: `grep -c " OO " restart_extraction.results/reactions_discovery.log`

   # Use the previous NetworkExtraction results to restart the ranking
   rm -rf restart_ranking.results
   AMS_JOBNAME=restart_ranking $AMSBIN/reactions_discovery << eor
       MolecularDynamics Enabled=No
       NetworkExtraction Enabled=No
       ProductRanking Enabled=Yes ReactionNetwork=restart_extraction.results
   eor

   #Test if ethanol is found:
   echo ETHANOL: `grep -c " CCO " restart_ranking.results/reactions_discovery.log`
   #Test if hydrogen peroxide is found:
   echo HYDROGEN PEROXIDE: `grep -c " OO " restart_ranking.results/reactions_discovery.log`

   # Demonstrate LatticeDeformation
   rm -rf complete_lattice_deformation.results

   AMS_JOBNAME=complete_lattice_deformation $AMSBIN/reactions_discovery << eor
      MolecularDynamics
         Enabled Yes
         NumSimulations 2
         BuildSystem
            NumAtoms 50
            Density 0.4
            Molecule 
               SMILES C[CH2]  # a CH3CH2 radical
               MoleFraction 1
            End
            Molecule 
               SMILES [OH]   # an OH radical
               MoleFraction 3
            End
         End
         Type LatticeDeformation
         LatticeDeformation
            NumCycles 3
            Temperature 500
            MinVolumeFraction 0.2
            Period 200
         End
         BondOrders Method=Guess
      End

      NetworkExtraction Enabled=Yes UseCharges=No
      ProductRanking Enabled=Yes

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

   #Test if ethanol is found:
   echo ETHANOL: `grep -c " CCO " complete_lattice_deformation.results/reactions_discovery.log`
   #Test if hydrogen peroxide is found:
   echo HYDROGEN PEROXIDE: `grep -c " OO " complete_lattice_deformation.results/reactions_discovery.log`

