#! /bin/sh


cat <<eor > H2O_on_MgO.xyz
39

O   0.0           0.0           0.0            region=H2O
H  -0.704320560   0.0          -0.66779884     region=H2O
H   0.704320560   0.0          -0.66779884     region=H2O
O   1.50158914    0.108856250  -2.19963815
O  -1.48731305    0.108246430  -2.19972248
Mg  0.00563782    1.59225904   -2.33893848
Mg  0.00352084   -1.44762418   -2.24965831
O   0.00696938    1.57832358   -4.42106808
O   0.00696938    4.55524313   -4.42106808
O   2.98388893   -1.39859597   -4.42106808
O   2.98388893    1.57832358   -4.42106808
O   2.98388893    4.55524313   -4.42106808
Mg -2.97355121   -1.39556394   -2.31959606
Mg -2.97743483    1.58619377   -2.31874087
Mg -2.97337639    4.55937829   -2.31649087
Mg  0.00549444    4.55739475   -2.31753869
Mg  2.98277888   -1.39600311   -2.32043545
Mg  2.98920147    1.58770902   -2.31910664
Mg  2.98383523    4.55827076   -2.31621824
O  -1.49388075   -2.89172181   -2.22718875
O  -1.48165368    3.06816545   -2.20685378
O   1.50285846   -2.89006842   -2.22921666
O   1.49233399    3.06893483   -2.20786341
O   4.47002638   -2.88279517   -2.21228396
O   4.47076537    0.09231531   -2.20652142
O   4.47074422    3.07217257   -2.21022983
Mg -1.48149039   -2.88705574   -4.42106808
Mg -1.48149039    0.08986381   -4.42106808
Mg -1.48149039    3.06678335   -4.42106808
Mg  1.49542915   -2.88705574   -4.42106808
Mg  1.49542915    0.08986381   -4.42106808
Mg  1.49542915    3.06678335   -4.42106808
Mg  4.47234870   -2.88705574   -4.42106808
Mg  4.47234870    0.08986381   -4.42106808
Mg  4.47234870    3.06678335   -4.42106808
O  -2.96995017   -1.39859597   -4.42106808
O  -2.96995017    1.57832358   -4.42106808
O  -2.96995017    4.55524313   -4.42106808
O   0.00696938   -1.39859597   -4.42106808
VEC1  8.93075865       0.00000000       0.00000000
VEC2  0.00000000       8.93075865       0.00000000
eor



AMS_JOBNAME=hessian $AMSBIN/ams << eor

Task SinglePoint
System
    GeometryFile H2O_on_MgO.xyz
End
Properties
    NormalModes Yes
    SelectedRegionForHessian H2O
End

NumericalDifferentiation
    NuclearStepSize 0.0001
End

Engine DFTB
    Model SCC-DFTB
    ResourcesDir DFTB.org/3ob-3-1
    DispersionCorrection D3-BJ
    KSpace Quality=GammaOnly
EndEngine
eor


AMS_JOBNAME=TS $AMSBIN/ams << eor

Task TransitionStateSearch

System
    GeometryFile H2O_on_MgO.xyz
End

Properties
    NormalModes Yes
    SelectedRegionForHessian H2O
End

GeometryOptimization
    Convergence Step=1.0e-3
    Quasi-Newton
       Step
           TrustRadius 0.015
       End
    End
    InitialHessian
        Type FromFile
        File hessian.results/dftb.rkf
    End
End

TransitionStateSearch
    ModeToFollow 1
End

Constraints
    Atom 4
    Atom 5
    Atom 6
    Atom 7
    Atom 8
    Atom 9
    Atom 10
    Atom 11
    Atom 12
    Atom 13
    Atom 14
    Atom 15
    Atom 16
    Atom 17
    Atom 18
    Atom 19
    Atom 20
    Atom 21
    Atom 22
    Atom 23
    Atom 24
    Atom 25
    Atom 26
    Atom 27
    Atom 28
    Atom 29
    Atom 30
    Atom 31
    Atom 32
    Atom 33
    Atom 34
    Atom 35
    Atom 36
    Atom 37
    Atom 38
    Atom 39
End

Engine DFTB
    Model SCC-DFTB
    ResourcesDir DFTB.org/3ob-3-1
    DispersionCorrection D3-BJ
    KSpace Quality=GammaOnly
EndEngine

eor


echo "Extract energy from the rkf file using amsreport:"
$AMSBIN/amsreport TS.results/dftb.rkf -r "AMSResults%Energy"

echo "Extract frequencies from the rkf file using amsreport:"
$AMSBIN/amsreport TS.results/dftb.rkf -r "Vibrations%Frequencies[cm-1]##1"