def mvplot_trajectories(self, colormap="hot", sampling=1, figure=None, show=True,
with_forces=True, **kwargs): # pragma: no cover
"""
Call mayavi_ to plot atomic trajectories and the variation of the unit cell.
"""
from abipy.display import mvtk
figure, mlab = mvtk.get_fig_mlab(figure=figure)
style = "labels"
line_width = 100
mvtk.plot_structure(self.initial_structure, style=style, unit_cell_color=(1, 0, 0), figure=figure)
mvtk.plot_structure(self.final_structure, style=style, unit_cell_color=(0, 0, 0), figure=figure)
steps = np.arange(start=0, stop=self.num_steps, step=sampling)
xcart_list = self.reader.read_value("xcart") * units.bohr_to_ang
for iatom in range(self.reader.natom):
x, y, z = xcart_list[::sampling, iatom, :].T
#for i in zip(x, y, z): print(i)
trajectory = mlab.plot3d(x, y, z, steps, colormap=colormap, tube_radius=None,
line_width=line_width, figure=figure)
mlab.colorbar(trajectory, title='Iteration', orientation='vertical')
if with_forces:
fcart_list = self.reader.read_cart_forces(unit="eV ang^-1")
for iatom in range(self.reader.natom):
x, y, z = xcart_list[::sampling, iatom, :].T
u, v, w = fcart_list[::sampling, iatom, :].T
q = mlab.quiver3d(x, y, z, u, v, w, figure=figure, colormap=colormap,
line_width=line_width, scale_factor=10)
#mlab.colorbar(q, title='Forces [eV/Ang]', orientation='vertical')
if show: mlab.show()
return figure
def mvplot_trajectories(self,
colormap="hot",
sampling=1,
figure=None,
show=True,
with_forces=True,
**kwargs): # pragma: no cover
"""
Call mayavi_ to plot atomic trajectories and the variation of the unit cell.
"""
from abipy.display import mvtk
figure, mlab = mvtk.get_fig_mlab(figure=figure)
style = "labels"
line_width = 100
mvtk.plot_structure(self.initial_structure,
style=style,
unit_cell_color=(1, 0, 0),
figure=figure)
mvtk.plot_structure(self.final_structure,
style=style,
unit_cell_color=(0, 0, 0),
figure=figure)
steps = np.arange(start=0, stop=self.num_steps, step=sampling)
xcart_list = self.reader.read_value("xcart") * units.bohr_to_ang
for iatom in range(self.reader.natom):
x, y, z = xcart_list[::sampling, iatom, :].T
#for i in zip(x, y, z): print(i)
trajectory = mlab.plot3d(x,
y,
z,
steps,
colormap=colormap,
tube_radius=None,
line_width=line_width,
figure=figure)
mlab.colorbar(trajectory,
title='Iteration',
orientation='vertical')
if with_forces:
fcart_list = self.reader.read_cart_forces(unit="eV ang^-1")
for iatom in range(self.reader.natom):
x, y, z = xcart_list[::sampling, iatom, :].T
u, v, w = fcart_list[::sampling, iatom, :].T
q = mlab.quiver3d(x,
y,
z,
u,
v,
w,
figure=figure,
colormap=colormap,
line_width=line_width,
scale_factor=10)
#mlab.colorbar(q, title='Forces [eV/Ang]', orientation='vertical')
if show: mlab.show()
return figure
def test_mayavi_toolkit(self):
"""Test mayavi toolkit."""
if not self.has_mayavi():
raise self.SkipTest("This test requires mayavi!")
figure, mlab = mvtk.get_fig_mlab(figure=None)
si_structure = self.get_abistructure_from_abiref("si_nscf_GSR.nc")
same_fig = mvtk.plot_wigner_seitz(si_structure.lattice, figure=figure)
assert same_fig is figure
figure = mvtk.plot_unit_cell(si_structure.lattice)
assert mvtk.plot_lattice_vectors(si_structure.lattice, figure=figure) is figure
assert mvtk.plot_structure(si_structure, frac_coords=False, to_unit_cell=False, style="points+labels",
unit_cell_color=(0, 0, 0), color_scheme="VESTA", figure=None, show=False)
def mvanimate(self, delay=500): # pragma: no cover
from abipy.display import mvtk
figure, mlab = mvtk.get_fig_mlab(figure=None)
style = "points"
#mvtk.plot_structure(self.initial_structure, style=style, figure=figure)
#mvtk.plot_structure(self.final_structure, style=style, figure=figure)
xcart_list = self.reader.read_value("xcart") * units.bohr_to_ang
#t = np.arange(self.num_steps)
#line_width = 2
#for iatom in range(self.reader.natom):
# x, y, z = xcart_list[:, iatom, :].T
# trajectory = mlab.plot3d(x, y, z, t, colormap=colormap, tube_radius=None, line_width=line_width, figure=figure)
#mlab.colorbar(trajectory, title='Iteration', orientation='vertical')
#x, y, z = xcart_list[0, :, :].T
#nodes = mlab.points3d(x, y, z)
#nodes.glyph.scale_mode = 'scale_by_vector'
#this sets the vectors to be a 3x5000 vector showing some random scalars
#nodes.mlab_source.dataset.point_data.vectors = np.tile( np.random.random((5000,)), (3,1))
#nodes.mlab_source.dataset.point_data.scalars = np.random.random((5000,))
@mlab.show
@mlab.animate(delay=delay, ui=True)
def anim():
"""Animate."""
for it, structure in enumerate(self.structures):
#for it in range(self.num_steps):
print('Updating scene for iteration:', it)
#mlab.clf(figure=figure)
mvtk.plot_structure(structure, style=style, figure=figure)
#x, y, z = xcart_list[it, :, :].T
#nodes.mlab_source.set(x=x, y=y, z=z)
#figure.scene.render()
mlab.draw(figure=figure)
yield
anim()
def mvanimate(self, delay=500): # pragma: no cover
from abipy.display import mvtk
figure, mlab = mvtk.get_fig_mlab(figure=None)
style = "points"
#mvtk.plot_structure(self.initial_structure, style=style, figure=figure)
#mvtk.plot_structure(self.final_structure, style=style, figure=figure)
xcart_list = self.reader.read_value("xcart") * units.bohr_to_ang
#t = np.arange(self.num_steps)
#line_width = 2
#for iatom in range(self.reader.natom):
# x, y, z = xcart_list[:, iatom, :].T
# trajectory = mlab.plot3d(x, y, z, t, colormap=colormap, tube_radius=None, line_width=line_width, figure=figure)
#mlab.colorbar(trajectory, title='Iteration', orientation='vertical')
#x, y, z = xcart_list[0, :, :].T
#nodes = mlab.points3d(x, y, z)
#nodes.glyph.scale_mode = 'scale_by_vector'
#this sets the vectors to be a 3x5000 vector showing some random scalars
#nodes.mlab_source.dataset.point_data.vectors = np.tile( np.random.random((5000,)), (3,1))
#nodes.mlab_source.dataset.point_data.scalars = np.random.random((5000,))
@mlab.show
@mlab.animate(delay=delay, ui=True)
def anim():
"""Animate."""
for it, structure in enumerate(self.structures):
#for it in range(self.num_steps):
print('Updating scene for iteration:', it)
#mlab.clf(figure=figure)
mvtk.plot_structure(structure, style=style, figure=figure)
#x, y, z = xcart_list[it, :, :].T
#nodes.mlab_source.set(x=x, y=y, z=z)
#figure.scene.render()
mlab.draw(figure=figure)
yield
anim()
def test_mayavi_toolkit(self):
"""Test mayavi toolkit."""
if not self.has_mayavi():
raise self.SkipTest("This test requires mayavi!")
figure, mlab = mvtk.get_fig_mlab(figure=None)
si_structure = self.get_abistructure_from_abiref("si_nscf_GSR.nc")
same_fig = mvtk.plot_wigner_seitz(si_structure.lattice, figure=figure)
assert same_fig is figure
figure = mvtk.plot_unit_cell(si_structure.lattice)
assert mvtk.plot_lattice_vectors(si_structure.lattice,
figure=figure) is figure
assert mvtk.plot_structure(si_structure,
frac_coords=False,
to_unit_cell=False,
style="points+labels",
unit_cell_color=(0, 0, 0),
color_scheme="VESTA",
figure=None,
show=False)