#!/bin/sh

export SCM_DISABLE_MPI=1

"$AMSBIN/ams" << eor

Task MolecularDynamics
MolecularDynamics
    NSteps 6500
    TimeStep 0.5
    Trajectory
        SamplingFreq 50
    End
    InitialVelocities
        Temperature 111
    End
    Thermostat
        Type Berendsen
        Temperature 300
        Tau 11.0
    End
    ReactionBoost
        Type RMSD
        NSteps 2000
        TargetSystem other_adsorption_site
        TargetSystem substitution_toplayer
        TargetSystem substitution_bottom_layer
        RMSDRestraint
            Type Harmonic
        End
    End
End
System
    Atoms
        Ag 2.449499704388572 2.35160228862905 -0.0162168072569689 
        Ag 3.879396827643018 4.340431494925371 -1.426236769294196 
        Ag 2.448295253965383 2.33796093956147 -2.873198576978953 
        Cu 6.739979767581435 4.34190611305328 1.077545301071925 region=Cu
        Ag 8.161563989474063 2.364152353698611 0.007293827282622109 
        Ag 8.152226184295738 6.315835942213118 -0.009428382852567571 
        Ag 1.019467943679718 0.3468664391937191 -1.412761628473732 
        Ag 8.166448501660387 6.352142717243685 -2.88487347591765 
        Ag 5.315334970205106 2.371584040270282 0.0003919710734874187 
        Ag 1.013224084104003 4.33841092345716 -1.426484027712664 
        Ag 5.311471342486222 6.310481596861236 -0.0008315062940891518 
        Ag 6.733785662132495 0.3453787646854145 -1.413983090143478 
        Ag 5.303223536847031 6.351429478244826 -2.882335562342726 
        Ag 6.735087198425579 4.339012281104702 -1.503755689343977 
        Ag 8.166566473166901 2.328510045039764 -2.883164369974275 
        Ag 2.444176524757417 6.329947836182889 -0.01987662145717678 
        Ag 3.877401873742306 0.3443171383856625 -1.411345408694745 
        Ag 2.446924595987084 6.343439409051821 -2.871901655988379 
        Ag 5.301876510135496 2.329631750538626 -2.884589121422461 
    End
    Lattice
        8.574802565214217 0.0 0.0
        0.0 7.993549281371378 0.0
    End
End
System other_adsorption_site
    Atoms
        Ag 2.443521824053424 2.364417724184156 -0.008315439626213516 
        Ag 3.868303552352363 4.333995687085758 -1.511588328333139 
        Ag 2.437996204664877 2.325890065949911 -2.889843515111663 
        Cu 3.85640405048869 4.337721855817676 1.074918440050592 
        Ag 8.155154918681049 2.3440488653745 -0.02395991229794923 
        Ag 8.157679568340866 6.327570016220148 -0.02630965704113123 
        Ag 1.011907760374722 0.3395352966523114 -1.42148249610441 
        Ag 8.157099512106921 6.337490933395778 -2.877917924978586 
        Ag 5.289862044166058 2.371734599078042 -0.004897335073915977 
        Ag 1.015245494735444 4.33494017151395 -1.43127654291252 
        Ag 5.298888354509224 6.296206977417001 -0.0108586225024408 
        Ag 6.722807152019262 0.3419269012582142 -1.416802595197964 
        Ag 5.301334305562885 6.345133355957811 -2.889235267678361 
        Ag 6.726412336083941 4.333283200517654 -1.433470976347663 
        Ag 8.157337060253711 2.334203577092884 -2.878401516868934 
        Ag 2.445127192394887 6.307004574078809 -0.009289553087657337 
        Ag 3.870824510149376 0.3387596941124601 -1.416953352694057 
        Ag 2.437790769838813 6.34565867077794 -2.88995133630551 
        Ag 5.300378051104217 2.326391229235759 -2.888758350765331 
    End
    Lattice
        8.574802565214217 0.0 0.0
        0.0 7.993549281371378 0.0
    End
End
System substitution_toplayer
    Atoms
        Ag 2.475331208269474 2.342680415969551 0.03304196684807805 
        Ag 3.872047104816491 4.312611869810816 -1.47335590186745 
        Ag 2.43119655948151 2.297586431107505 -2.833867837356515 
        Cu 5.268782167444299 6.268954050972728 -0.2359792423338486 
        Ag 8.173993167293927 2.301838514477176 0.004838148010488541 
        Ag 8.112854634647807 6.300617176451295 0.004618540447250827 
        Ag 1.011634696591691 0.3033013673880438 -1.379609276009462 
        Ag 8.155111620937786 6.303866168216331 -2.848285470384351 
        Ag 5.322742930625158 2.299149227992136 0.009014741905509861 
        Ag 1.01087528801193 4.31708389220921 -1.382234904706223 
        Ag 4.049929389006187 4.407843699955907 1.259178954240383 
        Ag 6.711453094650874 0.2751454919616778 -1.388229967916007 
        Ag 5.293070483971173 6.308319349647152 -2.910714640706277 
        Ag 6.711964127979507 4.324157474926375 -1.388272666155889 
        Ag 8.146732495249664 2.303755864527843 -2.818857265555564 
        Ag 2.471760573407767 6.304247023396688 0.003515864139251666 
        Ag 3.876127220190197 0.2988165322698367 -1.39278368301797 
        Ag 2.436023131954314 6.31312394748314 -2.868880712378035 
        Ag 5.297284945875642 2.295414925043033 -2.848625994945434 
    End
    Lattice
        8.574802565214217 0.0 0.0
        0.0 7.993549281371378 0.0
    End
End
System substitution_bottom_layer
    Atoms
        Ag 2.448289274498382 1.771341885834053 -0.1726747956060827 
        Ag 3.905635600418226 4.311459135065547 -0.6936661140435485 
        Ag 2.484242187761661 2.861268820108114 -2.689818423169725 
        Cu 6.770463230209981 4.302425310627667 -4.269448995820962 
        Ag 8.161851062029923 1.765769769779788 -0.1704126369397815 
        Ag 8.176309309952085 6.850425157052283 -0.1700438406603742 
        Ag 1.037431664411405 0.3123139120224849 -2.1691182430935 
        Ag 8.21509236023268 5.791177157225609 -2.703590178844768 
        Ag 5.312562042837024 1.763236417332867 -0.1702502840930947 
        Ag 1.046768906105167 4.307381154535485 -0.6853495704035901 
        Ag 5.325186985457115 6.846270939892302 -0.1793584128475504 
        Ag 6.746806378444587 0.3130040594468155 -2.17160972807291 
        Ag 5.315557324993655 5.78624069285866 -2.71384507221887 
        Ag 6.762440648184126 4.305500987021002 -0.7537109692600542 
        Ag 8.225312228771969 2.825811137742624 -2.707156225885198 
        Ag 2.460194947569557 6.849634769906135 -0.168318508527145 
        Ag 3.88398216845564 0.3114604747456248 -2.158591557904963 
        Ag 2.47693288637098 5.769562560359056 -2.683600245234852 
        Ag 5.317928090256332 2.826428471743946 -2.703949255396362 
    End
    Lattice
        8.574802565214217 0.0 0.0
        0.0 7.993549281371378 0.0
    End
End

Engine ASE
    Type Import
    Import ase.calculators.emt.EMT
EndEngine
eor