def radial_density(ion='Cl'):
s = current_system()
select_crystal()
center = cluster_center()
mask = s.type_array == ion | s.type_array == 'Na'
r_array = s.r_array.copy()
ions_r = r_array[mask]
ions_r -= center
ions_r = minimum_image(ions_r, s.box_vectors.diagonal())
# Density
mx = s.box_vectors.max()
# distance from center
distances = np.sqrt((ions_r ** 2).sum(axis=1))
bins = np.linspace(0, mx, 100)
hist, bins_= np.histogram(distances, bins)
# Normalize the histogram
start_shells_r = bins_[:-1]
end_shells_r = bins_[1:]
start_shells_V = 4.0/3.0 * np.pi * start_shells_r**3
end_shells_V = 4.0/3.0 * np.pi * end_shells_r**3
V_shell = end_shells_V - start_shells_V
return bins_[:-1], hist/V_shell
def center_on_crystal():
select_crystal()
center = cluster_center()
current_system().r_array -= center
current_system().r_array += 0.5 * current_system().box_vectors.diagonal()
current_system().r_array[:] = minimum_image(current_system().r_array, current_system().box_vectors.diagonal())
current_representation().update_positions(current_system().r_array)
def radial_density(ion='Cl'):
s = current_system()
select_crystal()
center = cluster_center()
mask = s.type_array == ion | s.type_array == 'Na'
r_array = s.r_array.copy()
ions_r = r_array[mask]
ions_r -= center
ions_r = minimum_image(ions_r, s.box_vectors.diagonal())
# Density
mx = s.box_vectors.max()
# distance from center
distances = np.sqrt((ions_r**2).sum(axis=1))
bins = np.linspace(0, mx, 100)
hist, bins_ = np.histogram(distances, bins)
# Normalize the histogram
start_shells_r = bins_[:-1]
end_shells_r = bins_[1:]
start_shells_V = 4.0 / 3.0 * np.pi * start_shells_r**3
end_shells_V = 4.0 / 3.0 * np.pi * end_shells_r**3
V_shell = end_shells_V - start_shells_V
return bins_[:-1], hist / V_shell
def center_on_crystal():
select_crystal()
center = cluster_center()
current_system().r_array -= center
current_system().r_array += 0.5 * current_system().box_vectors.diagonal()
current_system().r_array[:] = minimum_image(
current_system().r_array,
current_system().box_vectors.diagonal())
current_representation().update_positions(current_system().r_array)
def periodic_add(a, b):
return minimum_image(a + b,
current_system().box_vectors.diagonal())
def periodic_add(a, b):
return minimum_image(a + b, current_system().box_vectors.diagonal())
