def __init__(self, Moltemp_List, Composition_List, Box_Size, Name): self.Name = Name self.Moltemp_List = Moltemp_List self.Atom_Params, self.Bond_Params, self.Angle_Params, self.Dihedral_Params, self.Improper_Params = Molecule.Assign_Lammps( Moltemp_List) self.Composition_List = Composition_List self.Box_Size = Box_Size Num_Mol = 0 for Comp in self.Composition_List: Num_Mol += Comp print "Number of Molecules = ", Num_Mol self.Molecule_List = [] self.Current_Restart = "" self.Temperature = 800 return
def __init__(self, SAM, Surface, Num_SAMs, Box_Length, Name, Solvent=False): self.Name = Name self.SAM = SAM self.Surface = Surface self.Num_SAMs = Num_SAMs self.Box_Length = Box_Length self.Molecule_List = [] self.Current_Restart = "" self.Temperature = 400 if Solvent != False: self.Solvent = Solvent self.Solvent_Log = True self.Atom_Params, self.Bond_Params, self.Angle_Params, self.Dihedral_Params, self.Improper_Params = Molecule.Assign_Lammps( [SAM, Surface, Solvent]) else: self.Solvent_Log = False self.Atom_Params, self.Bond_Params, self.Angle_Params, self.Dihedral_Params, self.Improper_Params = Molecule.Assign_Lammps( [SAM, Surface]) return