from io import StringIO
from scm.plams import Molecule, Settings, AMSJob


def main(text):
    """
    The main script
    """
    # Read the molecule
    mol = Molecule()
    infile = StringIO(text)
    mol.readin(infile)

    # Set up the MD
    settings = Settings()
    settings.input.ams.Task = "MolecularDynamics"
    settings.input.ams.MolecularDynamics.NSteps = 1000
    settings.input.ams.MolecularDynamics.TimeStep = 0.5
    settings.input.ams.MolecularDynamics.Trajectory.SamplingFreq = 20
    settings.input.ams.MolecularDynamics.InitialVelocities.Temperature = 300
    settings.input.ams.MolecularDynamics.Thermostat.Type = "Berendsen"
    settings.input.ams.MolecularDynamics.Thermostat.Temperature = 300
    settings.input.ams.MolecularDynamics.Thermostat.Tau = 100
    settings.input.ams.MolecularDynamics.Checkpoint.Frequency = 10000
    settings.input.ForceField.Type = "Amber95"

    # Run the AMS MD simulation
    job = AMSJob(name="NaClwater", molecule=mol, settings=settings)
    results = job.run()
    print("Path to RKF file: ", results.rkfpath())


if __name__ == "__main__":

    text = """System
    Atoms
        Na -3.307984867989309 4.665211407614774 5.251579466053888 region=Builder ForceField.Type=IP ForceField.Charge=1.0
        Na 8.267368484754513 6.371503475665869 4.675660223754705 region=Builder ForceField.Type=IP ForceField.Charge=1.0
        Na 6.241897202502541 4.618148168402835 9.234796987012643 region=Builder ForceField.Type=IP ForceField.Charge=1.0
        Na -8.895532175785883 7.763596643004207 -1.173375402991997 region=Builder ForceField.Type=IP ForceField.Charge=1.0
        Na 4.915666374535903 -2.561076822189959 0.3832555477985536 region=Builder ForceField.Type=IP ForceField.Charge=1.0
        Cl 7.070220869477247 -3.385218397324887 9.253245004138604 region=Builder ForceField.Type=IM ForceField.Charge=-1.0
        Cl 1.311759721323258 -8.056121340180921 -9.099552022644028 region=Builder ForceField.Type=IM ForceField.Charge=-1.0
        Cl -1.117431383638206 5.554988508013128 1.806323657551233 region=Builder ForceField.Type=IM ForceField.Charge=-1.0
        Cl 3.189610452598285 -3.824547937385274 -6.081045625431574 region=Builder ForceField.Type=IM ForceField.Charge=-1.0
        Cl 4.029661290942884 -6.175591038156312 4.215897839800898 region=Builder ForceField.Type=IM ForceField.Charge=-1.0
        O -1.638965708475173 -8.304560335545137 -5.399693558676732 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -0.6989562096625178 -8.22251553741089 -5.682334495416144 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -1.653339195974134 -8.926973139338454 -4.67018111310851 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 4.098221341011048 -9.324362104466204 -0.4688960685713048 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 3.563523625411066 -9.257782892426816 0.3120785568129236 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 3.91882848966912 8.823085360652057 -0.7946630635994122 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -4.45122339013087 5.530300122404838 1.369645343758375 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -4.657332705123082 5.947520375003525 2.222436772005635 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -3.444509176723679 5.498843574899521 1.374285273753788 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -6.821864330063607 -9.549455340763965 -7.887741046214142 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -6.611693043632988 9.066394567694381 -8.764950866127899 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -6.020996290936347 9.191290101146935 -7.396952931897783 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 3.115938194336389 1.706670678588281 0.75342748805247 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 3.588709443846407 2.483860975299691 0.3600826352458891 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 3.768408187666474 1.005601043728181 0.6088977477118908 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -7.347047655632259 -7.668498533714922 6.93046708541403 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -7.79455932955915 -7.909942197495226 6.071785870916318 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -7.861870697126264 -6.915075398324899 7.155147467806739 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -4.503337847256558 0.03693223043156789 -4.415054901130072 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -3.979156080294072 -0.1094003199119583 -5.173059490583826 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -4.931990164904431 -0.8034225759521744 -4.279937279826926 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -6.369391544404177 -6.10314186387046 -8.992530096881882 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -5.620851229432827 -6.604234591239234 -9.38217121155313 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -7.043642638923164 -6.808551156696684 -9.047820094796243 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 0.003795549234116662 -8.638666495882209 0.7533331892872563 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -0.7687732343691029 -8.048802725322787 0.7320566650677496 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 0.6630965162591207 -8.04795162318919 1.221525397963397 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -2.34675756992035 8.930146130050767 3.660900310448933 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -2.047828401648621 8.088971770965957 4.076409493437286 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -1.628987752030673 -9.43105605645335 3.804586909279022 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 2.243828423325957 4.187991831161167 -6.484485056065208 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 2.318734683333163 4.160095076032141 -5.510574624857361 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 1.660169195180675 4.922495364843648 -6.627601127338433 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 2.174868606310292 7.560604226125383 -0.7480227941309863 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 1.343996462026106 7.202820033804404 -1.096922159209591 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 2.128286379615918 7.132485907329932 0.1391882318986387 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 3.189875650430659 8.744363396035048 2.196605255141561 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 2.269668019240405 8.621513810962995 2.566257659456736 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H -2.545447251074854 0.5882490015287007 -1.878307313299879 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -3.2036722558546 0.4628164178016149 -3.279517408997646 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 2.51402484625339 3.392359382905991 2.889843448143062 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 2.244755887164111 2.955999391680086 3.774732167570762 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 2.576142788186585 2.630362170148082 2.253936528652266 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H 4.921111904434225 -6.706761234377728 7.865952920031616 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 4.960531884006246 -7.753860192363071 6.831064025452655 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -5.370228113711227 1.661248382966231 7.436390144401797 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -5.236058212128718 1.797719939371765 8.342583625390578 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -5.584972979348956 0.7142419429228422 7.360020073371047 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 3.229025921594264 0.9165118808082244 -4.646837812546581 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 2.483384210950065 1.539348028384809 -4.84661209123323 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 2.799739531890971 0.2352588182111834 -4.132526382123689 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -7.104537747117833 -1.604665439769136 7.09122720219177 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -7.302660761249429 -1.728445454222934 8.029182231375154 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -7.80217187720903 -2.08206474966434 6.691987916921655 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 7.903959327752319 -9.503980448054964 -7.882247634441207 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H 7.185225939503872 -9.079568240542542 -7.338157229905846 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H 8.682653209019504 -9.322923473263142 -7.425216329788415 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O 5.646508616182192 1.789996279216629 5.015756231250863 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
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        H 5.553064245360971 0.8421867756155172 5.101413523188807 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H -8.320990512733774 6.885181153107787 -4.10984832965576 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -9.413438557329789 6.939882302078409 -5.182685497334365 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -3.364859281487327 9.048976363200067 -1.230039983984538 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -4.046842605646344 8.602971471578737 -1.839330745112465 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -2.662554798787731 8.368462536132574 -1.210952829695486 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -8.89795951156629 0.6720729387623189 0.65753524015 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -9.353348256114966 0.003419735233299131 1.214515427984513 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -8.406621029167026 1.23358674699581 1.262732738590238 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -8.064789778265373 -2.429394240165403 -3.788185433411088 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -8.030861838504011 -1.518865700036845 -4.24792017772699 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -8.898383013657865 -2.807521802683368 -4.115757647435903 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -9.049519259992675 7.062749689907633 6.262786776313596 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -9.264927171699613 7.583557274217552 7.056017086569412 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -8.123966308588837 6.835175459136886 6.285456694400072 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -4.096444002963606 9.091426320837344 -6.212791904244865 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -4.855314273034537 9.309276996749045 -5.582089961986176 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -3.52539052022688 -9.145714073280439 -6.168769990062334 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        O -5.026953026718775 5.194879531470495 9.34032350692863 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
        H -4.079277243361644 5.467743352484518 9.303721412557481 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -5.061543467564437 4.55383738170349 -8.893461143486421 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H -3.825406598307003 2.438569018321004 -1.228611174450658 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H 5.65552250070384 -8.937548205204251 -1.044157658231503 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H 0.1664519768327586 -5.007505178815621 -8.239983989208486 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H -4.248444977821295 -7.234984142053532 5.387550382031918 region=Builder ForceField.Type=HW ForceField.Charge=0.417
        H -5.104774279458531 -6.777647985277452 4.320544623975045 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H -7.756238065047726 -2.756270450497496 -0.009181373701427745 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        H 2.208698313381999 4.906703492306785 1.994038032397064 region=Builder ForceField.Type=HW ForceField.Charge=0.417
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        O -3.645740135013336 -0.6188784512558304 -6.8267967338453 region=Builder ForceField.Type=OW ForceField.Charge=-0.834
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        H 4.214153994518096 5.516069064428178 4.843028092657009 region=Builder ForceField.Type=HW ForceField.Charge=0.417
    End
    Lattice
        19.0 0.0 0.0
        0.0 19.0 0.0
        0.0 0.0 19.0
    End
    BondOrders
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    End
End"""
    main(text)