Initial work in the Molecule and Atom class

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

DPpack/SetGlobals.py

@@ -21,7 +21,7 @@ internal = {}
 ## Diceplayer:
 player['maxcyc'] = 1
 player['initcyc'] = 1        # May restart an optimization (append to geoms.xyz from start)
-player['nprocs'] = 1f
+player['nprocs'] = 1
 player['switchcyc'] = 3		 # At which step start doing only one QM calculation (geom & chg)
 player['altsteps'] = 20000   # Steps for thermalization when starting from previous step
 player['maxstep'] = 0.3      # Maxstep for geometry relaxation in Bohr

DPpack/SetGlobalsClass.py

@@ -0,0 +1,49 @@
+import os, sys
+import math
+import shutil
+import textwrap
+import numpy as np
+
+from DPpack.PTable import *
+from DPpack.Misc import *
+
+class Molecule:
+
+	def __init__(self):
+
+		self.atoms = []					# Lista de instancias de Atom
+		self.positions = None			# Array Numpy
+		self.energy = None				# Array Numpy
+		self.gradient = None			# Array Numpy
+		self.hessian = None				# Array Numpy
+
+	def add_atom(self, a):
+
+		self.atoms.append(a)			# Inserção de um novo atomo
+
+	def center_of_mass(self):
+	
+		com = np.zeros(3)
+		total_mass = 0.0
+		for atom in self.atoms:
+			total_mass += atom.mass
+			com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
+		
+		com = com / total_mass
+		
+		return com
+
+
+class Atom:
+
+	def __init__(self, lbl,na,rx,ry,rz,chg,eps,sig):
+		
+		self.lbl = lbl                  # Integer
+		self.na = na                    # Integer
+		self.rx = rx                    # Double
+		self.ry = ry                    # Double
+		self.rz = rz                    # Double
+		self.chg = chg                  # Double
+		self.eps = eps                  # Double
+		self.sig = sig                  # Double
+		self.mass = atommass[self.na]   # Double