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from ase.io.utils import PlottingVariables, make_patch_list
class Matplotlib(PlottingVariables):
def __init__(self, atoms, ax,
rotation='', radii=None,
colors=None, scale=1, offset=(0, 0), **parameters):
PlottingVariables.__init__(
self, atoms, rotation=rotation,
radii=radii, colors=colors, scale=scale,
extra_offset=offset, **parameters)
self.ax = ax
self.figure = ax.figure
self.ax.set_aspect('equal')
def write(self):
self.write_body()
self.ax.set_xlim(0, self.w)
self.ax.set_ylim(0, self.h)
def write_body(self):
patch_list = make_patch_list(self)
for patch in patch_list:
self.ax.add_patch(patch)
def animate(images, ax=None,
interval=200, # in ms; same default value as in FuncAnimation
save_count=None, # ignored as of 2023 with newer matplotlib
**parameters):
"""Convert sequence of atoms objects into Matplotlib animation.
Each image is generated using plot_atoms(). Additional parameters
are passed to this function."""
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
if ax is None:
ax = plt.gca()
fig = ax.get_figure()
def drawimage(atoms):
ax.clear()
ax.axis('off')
plot_atoms(atoms, ax=ax, **parameters)
animation = FuncAnimation(fig, drawimage, frames=images,
init_func=lambda: None,
interval=interval)
return animation
def plot_atoms(atoms, ax=None, **parameters):
"""Plot an atoms object in a matplotlib subplot.
Parameters
----------
atoms : Atoms object
ax : Matplotlib subplot object
rotation : str, optional
In degrees. In the form '10x,20y,30z'
show_unit_cell : int, optional, default 2
Draw the unit cell as dashed lines depending on value:
0: Don't
1: Do
2: Do, making sure cell is visible
radii : float, optional
The radii of the atoms
colors : list of strings, optional
Color of the atoms, must be the same length as
the number of atoms in the atoms object.
scale : float, optional
Scaling of the plotted atoms and lines.
offset : tuple (float, float), optional
Offset of the plotted atoms and lines.
"""
if isinstance(atoms, list):
assert len(atoms) == 1
atoms = atoms[0]
import matplotlib.pyplot as plt
if ax is None:
ax = plt.gca()
Matplotlib(atoms, ax, **parameters).write()
return ax
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