files=['Cl_pulse_1.hdf5','Cl_pulse_1.hdf5','Cl_pulse_3.hdf5','Cl_pulse_4.hdf5']
monolayer=16
hook=CleanVacuumRegion()
for file in files:
    sps=nlread(file,SurfaceProcessSimulation)[-1]
    traj=sps.trajectories()
    primitive=traj[0].lastImage().primitiveVectors()
    area=numpy.linalg.norm(numpy.cross(primitive[0].inUnitsOf(Ang),primitive[1].inUnitsOf(Ang)))*Angstrom**2
    fluence=[]
    uptake=[]
    for i in range(0,len(traj)):
        conf=traj[i].lastImage()
        hook._apply(conf)
        sym=conf.symbols()
        count=sym.count('Cl')
        fluence.append(i/area)
        uptake.append(count/monolayer)
    # PlotModel with custom units.
    model = Plot.PlotModel(x_unit=nm**-2)

    # Set axis label and scale
    model.xAxis().setLabel('Fluence')
    model.yAxis().setLabel('Uptake [ML]')

    #Line.
    line = Plot.Line(fluence,uptake)
    line.setColor('red')

    # Add line.
    model.addItem(line)

    # Auto-adjust axis limits.
    model.setLimits()

    # Show plot and save afterwards to file and as raster.
    Plot.show(model)
    Plot.save(model, file)