def calculateProperties(timestepData, atoms): properties = Properties() timestepData["molecule"] = {} timestepData["molecule"]["moleculeList"] = properties.findStructure( atoms, timestepData["position"], consts.cutoff) #init data lists in timestep data timestepData["molecule"]["RKE"] = [] timestepData["molecule"]["KE"] = [] timestepData["molecule"]["TKE"] = [] timestepData["molecule"]["VelocityCOM"] = [] timestepData["molecule"]["KECOM"] = [] for molecule in timestepData["molecule"]["moleculeList"]: # timestepData["molecule"]["RKE"].append(properties.RKE(molecule,atoms,timestepData["position"],timestepData["velocity"])) timestepData["molecule"]["TKE"].append( properties.TKE(molecule, atoms, timestepData["velocity"])) Vcom = properties.Vcom(molecule, atoms, timestepData["velocity"]) timestepData["molecule"]["VelocityCOM"].append(Vcom) timestepData["molecule"]["KECOM"].append( properties.KEcom(molecule, atoms, Vcom)) return timestepData