#!/bin/sh


# 1. Replay of PES scans
# ======================

AMS_JOBNAME=pesscan "$AMSBIN/ams" << eor

Task PESScan

PESScan
    ScanCoordinate
        nPoints 6
        Dihedral 5 1 2 6 0.0 50
        Dihedral 4 1 2 3 0.0 50
    End
    ScanCoordinate
        nPoints 7
        Distance 1 2 1.2 1.5
    End
End

System
    Atoms
        C 0.0 -0.0 0.66687
        C 0.0 -0.0 -0.33313
        H 0.0 0.92974 -0.90538
        H 0.0 0.92974 1.23912
        H 0.0 -0.92974 1.23912
        H 0.0 -0.92974 -0.90538
    End
End

Engine ForceField
EndEngine

eor


AMS_JOBNAME=replay_pesscan "$AMSBIN/ams" << eor

Task Replay
Replay
   File pesscan.results
   StoreAllResultFiles Yes
End

Properties
   Gradients True
End

Engine DFTB
EndEngine

eor


echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 42 ]; do   
   echo "Frame: $frame"
   $AMSBIN/amsreport replay_pesscan.results/ams.rkf -r "History%Energy($frame)"
   $AMSBIN/amsreport replay_pesscan.results/ams.rkf -r "History%Gradients($frame)"
   frame=$(expr $frame + 1)
   

done
echo "Data in PESScan section:"
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%PESCoords'
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%PES'
$AMSBIN/amsreport replay_pesscan.results/ams.rkf -r 'PESScan%HistoryIndices'
echo "Data extracted."


# 2. Replay of NEB calculations
# =============================

AMS_JOBNAME=neb "$AMSBIN/ams" << eor

Task NEB

NEB
    Images 16
End

GeometryOptimization
   Convergence
      Energy 1.0e-4
      Gradients 1.0e-2
   End
End

System
    Atoms
        C -0.04837097189972882 0.002828754545985427 1.099927275387085
        C -0.7231327687579711 -1.264630955508361 1.591341080262239
        C -0.7174118987979032 1.275587203448819 1.585489846719994
        H -1.758221225827696 -1.294861009536393 1.215612210647893
        H -0.7536609466556244 -1.286949469754588 2.689737906089842
        H 0.02700743800283175 0.0001348498227195367 0.004547638456250216
        H -0.7481941882345999 1.302956664081095 2.683766567353197
        H -0.1880537663322776 2.167332127899618 1.228056629315197
        H -1.752232117403696 1.308927696210993 1.209290912745431
        H -0.1979764470101184 -2.160385916691095 1.237731888775011
        Cl 1.710726893919094 4.005547128448699e-05 1.649098041095717
    End
End
System final
    Atoms
        C -0.8173023574499557 -0.01408167289928656 0.8544841004283144
        C -1.086263680920393 -1.14724517989661 1.518039806717775
        C -0.8990221290639472 1.362120508644236 1.43231282384412
        H -1.018446188967536 -2.121649215821082 1.03173453221026
        H -1.404982357822256 -1.129945575549278 2.563696578967125
        H -0.5085933307712909 -0.08344191227560969 -0.1948268157146379
        H -1.210244367762068 1.342173382164807 2.485525533439326
        H 0.07413947140246446 1.873805664554979 1.364278897383801
        H -1.616521025856608 1.9769362830809 0.8657976784252567
        H 1.044986335480545 -0.9543604705303219 1.922869894354733
        Cl 2.292729632733364 -1.053331811482705 2.350686966791855
    End
End

Engine DFTB
EndEngine

eor


AMS_JOBNAME=replay_neb "$AMSBIN/ams" << eor

Task Replay
Replay File=neb.results/ams.rkf

Engine ADF
   NumericalQuality Basic
EndEngine

eor


echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 16 ]; do
   echo "Frame: $frame"      
   $AMSBIN/amsreport replay_neb.results/ams.rkf -r "History%Energy($frame)"
   frame=$(expr $frame + 1)
done
echo "Data in NEB section:"
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%nebIterations'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%historyIndex@dim'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%historyIndex'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%energy'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%highestIndex'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%LeftBarrier'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%RightBarrier'
$AMSBIN/amsreport replay_neb.results/ams.rkf -r 'NEB%ReactionEnergy'
echo "Data extracted."


# 3. Replay of generic history (e.g. MD)
# ======================================

AMS_JOBNAME=md "$AMSBIN/ams" << eor

Task MolecularDynamics

MolecularDynamics
   nSteps 1000
   InitialVelocities Type=Zero
   Trajectory SamplingFreq=10
End

System
   Atoms
      O       5.84400000       0.31970000       0.89540000
      H       1.17000000       0.12750000      -2.13090000
      H      -0.61000000      -1.28280000      -1.84810000
      H      -0.57930000      -0.70680000       1.15800000
      C      -3.12520000       0.09550000       0.94430000
      C      -3.19980000      -1.42460000       1.23360000
      C      -2.05280000       0.23760000      -0.14210000
      C      -1.27100000       1.53130000      -0.13370000
      C      -0.13080000       1.46490000      -1.14670000
      C      -2.05030000      -2.08490000       0.42320000
      C      -1.08120000      -0.91390000       0.20520000
      C       0.72590000       0.20890000      -1.09890000
      C      -0.07070000      -1.07000000      -0.90020000
      C       1.91880000       0.37840000      -0.17010000
      C       2.85070000       1.44940000      -0.76420000
      C       4.06090000       1.66070000       0.14280000
      C       0.79940000      -2.27110000      -0.66800000
      C       2.70610000      -0.90160000      -0.05510000
      C       4.70630000       0.33980000       0.46480000
      C       2.06470000      -2.18950000      -0.28730000
      C       4.02370000      -0.86790000       0.26480000
      C       1.49560000       0.82380000       1.22970000
      C      -2.72010000       0.03450000      -1.50220000
      C      -4.44990000       0.59620000       0.43260000
      O      -5.21170000      -0.16370000      -0.11570000
      C      -4.82510000       2.04560000       0.60460000
      H      -2.82710000       0.64000000       1.83720000
      H      -3.05600000      -1.60950000       2.29900000
      H      -4.16120000      -1.82340000       0.91220000
      H      -1.95080000       2.35390000      -0.41170000
      H      -0.90510000       1.74180000       0.87040000
      H      -0.54560000       1.56290000      -2.16020000
      H       0.51310000       2.34310000      -1.00320000
      H      -1.56740000      -2.86790000       1.01220000
      H      -2.40770000      -2.48600000      -0.52040000
      H       3.18420000       1.11610000      -1.74960000
      H       2.30420000       2.38610000      -0.86930000
      H       4.79290000       2.28810000      -0.38330000
      H       3.77550000       2.17310000       1.05860000
      H       0.36740000      -3.25490000      -0.82120000
      H       2.63690000      -3.09890000      -0.14660000
      H       4.55990000      -1.80060000       0.37040000
      H       0.83020000       0.07700000       1.66290000
      H       2.37890000       0.93230000       1.85900000
      H       0.97580000       1.77970000       1.16520000
      H      -3.42010000       0.84890000      -1.68870000
      H      -1.95890000       0.02380000      -2.28240000
      H      -3.25700000      -0.91410000      -1.50550000
      H      -4.48270000       2.61460000      -0.25970000
      H      -5.90820000       2.13270000       0.69120000
      H      -4.35580000       2.43770000       1.50690000
   End
End

Engine ReaxFF
   ForceField CHON-2019.ff
EndEngine

eor


AMS_JOBNAME=replay_md "$AMSBIN/ams" << eor

Task Replay
Replay
   File md.results/
   Frames 1:101:10
End

Properties
   Gradients True
   BondOrders True
End

Engine DFTB
EndEngine

eor


echo "Start extracting data from ams.rkf ..."
echo "Number of frames on file:"
$AMSBIN/amsreport replay_md.results/ams.rkf -r 'History%nEntries'
frame=1
while [ $frame -le 11 ]; do   
   echo "Frame: $frame"
   $AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Energy($frame)"
   $AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Index($frame)"
   $AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Atoms($frame)"
   $AMSBIN/amsreport replay_md.results/ams.rkf -r "History%Bonds.Orders($frame)#8.2f"
   frame=$(expr $frame + 1)
done
echo "Data extracted."