Vitor Hideyoshi Nakazone Batista
292995d0ea
Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
50 lines
1.1 KiB
Python
50 lines
1.1 KiB
Python
import os, sys
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import math
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import shutil
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import textwrap
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import numpy as np
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from DPpack.PTable import *
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from DPpack.Misc import *
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class Molecule:
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def __init__(self):
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self.atoms = [] # Lista de instancias de Atom
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self.positions = None # Array Numpy
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self.energy = None # Array Numpy
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self.gradient = None # Array Numpy
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self.hessian = None # Array Numpy
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def add_atom(self, a):
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self.atoms.append(a) # Inserção de um novo atomo
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def center_of_mass(self):
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com = np.zeros(3)
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total_mass = 0.0
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for atom in self.atoms:
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total_mass += atom.mass
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com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
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com = com / total_mass
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return com
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class Atom:
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def __init__(self, lbl,na,rx,ry,rz,chg,eps,sig):
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self.lbl = lbl # Integer
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self.na = na # Integer
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self.rx = rx # Double
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self.ry = ry # Double
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self.rz = rz # Double
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self.chg = chg # Double
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self.eps = eps # Double
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self.sig = sig # Double
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self.mass = atommass[self.na] # Double
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