Dice Player Translation, Initial work on Dice Processes

This commit adds the functions responsible for creating Dice inputs and calling dice it self, the original functions were removed from the Dice.py file and added to SetGlobals' Internal and Dice classes

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>

DPpack/MolHandling.py

@@ -21,11 +21,11 @@ ang2bohr = 1/bohr2ang
 class System:
 
 	def __init__(self):
-		
+
 		self.molecule = []
 		self.nmols = []
 
-	def add_type(self,nmols, m):
+	def add_type(self, nmols, m):
 		
 		self.molecule.append(m)
 		self.nmols.append(nmols)
@@ -189,21 +189,30 @@ class System:
 
 class Molecule:
 
-	def __init__(self):
+	def __init__(self, molname):
+
+		self.molname = molname
 
 		self.atom = []					# Lista de instancias de Atom
 		self.position = None			# Array Numpy
 		self.energy = None				# Array Numpy
 		self.gradient = None			# Array Numpy
 		self.hessian = None				# Array Numpy
+
 		self.total_mass = 0
 		self.com = None
+		self.ghost_atoms = [] # Stores the index of the ghost atoms in the atoms array
+		self.lp_atoms = []
 
 	def add_atom(self, a):
 
 		self.atom.append(a)			# Inserção de um novo atomo
 		self.total_mass += a.mass
 
+		if (a.na == ghost_number):
+
+			self.ghost_atoms.append(self.atom.index(a))
+
 		self.center_of_mass()
 
 	def center_of_mass(self):