From 292995d0eac228ecc4b0a2e6d8283b35edf33c0b Mon Sep 17 00:00:00 2001
From: Vitor Hideyoshi Nakazone Batista <vitor.h.n.batista@gmail.com>
Date: Tue, 29 Jun 2021 17:16:00 -0300
Subject: [PATCH] Initial work in the Molecule and Atom class

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
---
 .vscode/settings.json     |  3 +++
 DPpack/SetGlobals.py      |  2 +-
 DPpack/SetGlobalsClass.py | 49 +++++++++++++++++++++++++++++++++++++++
 diceplayer.py             |  1 +
 4 files changed, 54 insertions(+), 1 deletion(-)
 create mode 100644 .vscode/settings.json
 create mode 100644 DPpack/SetGlobalsClass.py

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..52e1068
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": "/home/hideyoshi/Python/3.8/bin/python3.8"
+}
\ No newline at end of file
diff --git a/DPpack/SetGlobals.py b/DPpack/SetGlobals.py
index 61fd7dd..6fb4c8a 100644
--- a/DPpack/SetGlobals.py
+++ b/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
diff --git a/DPpack/SetGlobalsClass.py b/DPpack/SetGlobalsClass.py
new file mode 100644
index 0000000..63b6022
--- /dev/null
+++ b/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
diff --git a/diceplayer.py b/diceplayer.py
index e9cb51e..fb79f77 100644
--- a/diceplayer.py
+++ b/diceplayer.py
@@ -23,6 +23,7 @@ if __name__ == '__main__':
     			                   help='input file of diceplayer [default = control.in]')
 	parser.add_argument('-o', dest='outfile', default='run.log', metavar='OUTFILE', 
     				                 help='output file of diceplayer [default = run.log]')
+	## Study the option of a parameter for continuing the last process via data from control.in and run.log files
 
 	args = parser.parse_args()