def center_mass(self, list_of_atoms=None):
"""
Computes the center of mass (CM) of the XYZ object or
a partial list of atoms. The default is to compute the
CM of all the atoms in the object, if a list
is enter only those in the list will be included for the CM
Return the CM as a numpy array
"""
if list_of_atoms is None:
list_of_atoms = range(self.natom)
total_mass = 0.0
center_of_mass = np.zeros(3)
if self.natom == 0:
return center_of_mass
atomicnumber = atomic_number(list(self.symbols))
for i in range(self.natom):
if i in list_of_atoms:
total_mass = total_mass + mass(atomicnumber[i])
center_of_mass = center_of_mass + mass(
atomicnumber[i]) * self.positions[i]
return center_of_mass / total_mass
def product_of_inertia(self, axis):
assert self.is_perfect
I = 0
for isite in self:
I += mass(isite.symbols[0]) * (np.prod(isite.position) / isite.position[axis])
return I
def moment_of_inertia(self, axis):
assert self.is_perfect
I = 0
for isite in self:
I += mass(isite.symbols[0]) * (sum(isite.position ** 2) - isite.position[axis] ** 2)
return I
def density(self):
"""
Computes the density of the cell
:rtype : float
"""
return sum(_np.array(mass(self.symbols))) / self.volume
def product_of_inertia(self, axis):
assert self.is_perfect
I = 0
for isite in self:
I += mass(isite.symbols[0]) * (np.prod(isite.position) /
isite.position[axis])
return I
def moment_of_inertia(self, axis):
assert self.is_perfect
I = 0
for isite in self:
I += mass(isite.symbols[0]) * (sum(isite.position**2) -
isite.position[axis]**2)
return I
def moment_of_inertia(self, axis):
assert self.is_perfect
mofi = 0
for isite in self:
mofi += mass(isite.symbols[0]) * (
sum(np.array(isite.position)**2) - isite.position[axis]**2)
return mofi
def density(self):
"""
Computes the density of the cell
:rtype: float
:return: float
"""
return sum(np.array(mass(self.symbols))) / self.volume
def steepest_descent(self, dt=1, tolerance=1E-3):
forces = self.get_forces()
while np.max(self.get_magnitude_forces()) > tolerance:
for i in range(self.structure.natom):
imass = mass(self.structure.symbols[i])
self.structure.positions[i] += 0.5 * forces[i] / imass * dt ** 2
forces = self.get_forces()
maxforce = np.max(self.get_magnitude_forces())
dt = max(100.0 / maxforce, 1.0)
pcm_log.debug('Steepest Descent maxforce= %9.3E density=%7.4f dt=%7.3f' % (maxforce,
self.structure.density, dt))
def steepest_descent(self, dt=1, tolerance=1E-3):
forces = self.get_forces()
while np.max(self.get_magnitude_forces()) > tolerance:
for i in range(self.structure.natom):
imass = mass(self.structure.symbols[i])
self.structure.positions[i] += 0.5 * forces[i] / imass * dt**2
forces = self.get_forces()
maxforce = np.max(self.get_magnitude_forces())
dt = max(100.0 / maxforce, 1.0)
pcm_log.debug(
'Steepest Descent maxforce= %9.3E density=%7.4f dt=%7.3f' %
(maxforce, self.structure.density, dt))
def center_mass(self, list_of_atoms=None):
"""
Computes the center of mass (CM) of the XYZ object or
a partial list of atoms. The default is to compute the
CM of all the atoms in the object, if a list
is enter only those in the list will be included for the CM
Return the CM as a numpy array
"""
if list_of_atoms is None:
list_of_atoms = range(self.natom)
total_mass = 0.0
center_of_mass = np.zeros(3)
if self.natom == 0:
return center_of_mass
atomicnumber = atomic_number(list(self.symbols))
for i in range(self.natom):
if i in list_of_atoms:
total_mass = total_mass + mass(atomicnumber[i])
center_of_mass = center_of_mass + mass(atomicnumber[i]) * self.positions[i]
return center_of_mass / total_mass