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SetGlobas/MolHandling(fixes)/DicePlayer Translation

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Fixed Numerus functions in the SetGlobals file and MolHandling, translated DicePlayer and tested till, such as inertia_tensor, add_type, center_of_mass_to_origin. standard_orientation; and removed chglevel keyword

Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
Vitor Hideyoshi
2021-10-24 00:55:11 -03:00
committed by Vitor Hideyoshi
parent 316acf4761
commit 6017f272b3
5 changed files with 64 additions and 77 deletions
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68
DPpack/MolHandling.py
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@@ -28,7 +28,7 @@ class System:
def add_type(self,nmols, m):
self.molecule.append(m)
self.nmols = nmols
self.nmols.append(nmols)
# Função que calcula a distância entre dois centros de massa
# e por se tratar de uma função de dois atomos não deve ser
@@ -208,21 +208,17 @@ class Molecule:
def center_of_mass(self):
com = np.zeros(3)
total_mass = 0.0
self.com = np.zeros(3)
for atom in self.atom:
total_mass += atom.mass
com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
self.com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
com = com / total_mass
self.com = com
self.com = self.com / self.total_mass
def center_of_mass_to_origin(self):
com = self.center_of_mass()
self.center_of_mass()
for atom in self.atom:
@@ -260,6 +256,30 @@ class Molecule:
return np.array(distances).reshape(dim, dim)
def inertia_tensor(self):
self.center_of_mass()
Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
for atom in self.atom:
#### Obtain the displacement from the center of mass
dx = atom.rx - self.com[0]
dy = atom.ry - self.com[1]
dz = atom.rz - self.com[2]
#### Update the diagonal components of the tensor
Ixx += atom.mass * (dy**2 + dz**2)
Iyy += atom.mass * (dz**2 + dx**2)
Izz += atom.mass * (dx**2 + dy**2)
#### Update the off-diagonal components of the tensor
Ixy += atom.mass * dx * dy * -1
Ixz += atom.mass * dx * dz * -1
Iyz += atom.mass * dy * dz * -1
return np.array([[Ixx, Ixy, Ixz],
[Ixy, Iyy, Iyz],
[Ixz, Iyz, Izz]])
def eixos(self):
eixos = np.zeros(3)
@@ -288,36 +308,13 @@ class Molecule:
return eixos
def inertia_tensor(self):
Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
for atom in self.atom:
#### Obtain the displacement from the center of mass
dx = atom.rx - self.com[0]
dy = atom.ry - self.com[1]
dz = atom.rz - self.com[2]
#### Update the diagonal components of the tensor
Ixx += atom.mass * (dy**2 + dz**2)
Iyy += atom.mass * (dz**2 + dx**2)
Izz += atom.mass * (dx**2 + dy**2)
#### Update the off-diagonal components of the tensor
Ixy += atom.mass * dx * dy * -1
Ixz += atom.mass * dx * dz * -1
Iyz += atom.mass * dy * dz * -1
return np.array([ [Ixx, Ixy, Ixz],
[Ixy, Iyy, Iyz],
[Ixz, Iyz, Izz] ])
def principal_axes(self):
try:
evals, evecs = linalg.eigh(self.inertia_tensor())
except:
sys.exit("Error: diagonalization of inertia tensor did not converge")
return evals, evecs
def read_position(self):
@@ -366,7 +363,6 @@ class Molecule:
def standard_orientation(self):
self.center_of_mass_to_origin()
tensor = self.inertia_tensor()
evals, evecs = self.principal_axes()
if round(linalg.det(evecs)) == -1:
@@ -435,6 +431,4 @@ class Atom:
self.chg = chg # Double
self.eps = eps # Double
self.sig = sig # Double
self.mass = atommass[self.na] # Double
self.mass = atommass[self.na] # Double