def Render(Frac, Bead, Dens):
data = import_file('./../frac_' + str(Frac) + '/m_' + str(Bead) + '/d_' +
str(Dens) + '/final_snapshot.xyz')
data.add_to_scene()
vis_element = data.source.data.particles.vis
vis_element.radius = .9
cell_vis = data.source.data.cell.vis
cell_vis.render_cell = False
vp = Viewport(type=Viewport.Type.Bottom)
vp.zoom_all(size=(600, 500))
image = vp.render_image(size=(600, 500), alpha=True)
image.save("f-" + str(int((1 - Frac) * 10 % 10)) + "/b-" + str(Bead) +
"_d-" + str(Dens) + ".png")
data.remove_from_scene()
def Render1(item, Renderer, selector0, delector):
pipeline = import_file('./../frac_' + str(item[0]) + '/m_' + str(item[1]) +
'/d_' + str(item[2]) + '/final_snapshot.xyz')
pipeline.modifiers.append(selector0)
pipeline.modifiers.append(delector)
pipeline.add_to_scene()
vis_element = pipeline.source.data.particles.vis
vis_element.radius = .5
cell_vis = pipeline.source.data.cell.vis
cell_vis.render_cell = False
vp = Viewport(type=Viewport.Type.Left)
vp.zoom_all(size=(600, 500))
image = vp.render_image(size=(600, 500), alpha=True, renderer=Renderer)
image.save("f-" + str(int((1 - item[0]) * 10 % 10)) + "/rand/b-" +
str(item[1]) + "_d-" + str(item[2]) + "(phobic).png")
pipeline.remove_from_scene()
def show_ovito(particle,
cell,
outfile=None,
radius=0.35,
viewport=None,
callback=None,
tmpdir=None,
camera_dir=(0, 1, 0),
camera_pos=(0, -10, 0),
size=(640, 480),
zoom=True,
perspective=False):
"""
Render particle in cell using ovito
"""
import os
try:
from ovito.io import import_file
except ImportError:
_log.warning('install ovito to display the particles')
return
from ovito.vis import Viewport, TachyonRenderer
from ovito.vis import ParticlesVis
import tempfile
from atooms.core.utils import mkdir
# Make sure dirname exists
if outfile is not None:
mkdir(os.path.dirname(outfile))
# Get a temporary file to write the sample
fh = tempfile.NamedTemporaryFile('w',
dir=tmpdir,
suffix='.xyz',
delete=False)
tmp_file = fh.name
# Self-contained EXYZ dump (it is not clean to use trajectories here)
fh.write('{}\n'.format(len(particle)))
fh.write(
'Properties=species:S:1:pos:R:3 Lattice="{},0.,0.,0.,{},0.,0.,0.,{}"\n'
.format(*cell.side))
for p in particle:
fh.write('{} {} {} {}\n'.format(p.species, *p.position))
fh.close()
# Ovito stuff. Can be customized by client code.
pipeline = import_file(tmp_file)
# Ovito seems to ignore the lattice info of exyz file
# so we forcibly set the cell info here
pipeline.source.data.cell_[0, 0] = cell.side[0]
pipeline.source.data.cell_[1, 1] = cell.side[1]
pipeline.source.data.cell_[2, 2] = cell.side[2]
pipeline.source.data.cell_[:, 3] = -cell.side / 2
# Scale radius by default
vis_element = pipeline.source.data.particles.vis
vis_element.radius = radius
# Apply client code callback
if callback:
callback(pipeline)
pipeline.add_to_scene()
# Define viewport
if viewport:
vp = vieport
else:
if perspective:
vp = Viewport(type=Viewport.Type.Perspective,
camera_dir=camera_dir,
camera_pos=camera_pos)
else:
vp = Viewport(type=Viewport.Type.Ortho,
camera_dir=camera_dir,
camera_pos=camera_pos)
# Render
if zoom:
vp.zoom_all()
if outfile is None:
outfile = tmp_file + '.png'
vp.render_image(filename=outfile, size=size, renderer=TachyonRenderer())
# Scene is a singleton, so we must clear it
pipeline.remove_from_scene()
from atooms.core.utils import rmf
rmf(tmp_file)
# Try to display the image (e.g. in a jupyter notebook)
try:
from IPython.display import Image
return Image(outfile)
except ImportError:
return outfile
def ovito_view(sample_path, filename, view="Perspective"):
"""
Use the package ovito to make visualizaitons of molecules.
Parameters
----------
sample_path : str
The path of the file to visualize
filename : str
The name of the output file image
view : str (optional)
The view to use
"""
if use_ovito:
# Import the sample file.
pipeline = import_file(sample_path)
pipeline.source.data.cell.vis.enabled = False
pipeline.source.data.particles.vis.radius = 0.5
pipeline.add_to_scene()
vp = Viewport()
if view == "Perspective":
vp.type = Viewport.Type.Perspective
vp.camera_dir = (-1, -1, -1)
elif view == "Ortho":
vp.type = Viewport.Type.Ortho
vp.camera_dir = (-1, -1, -1)
elif view == "Top":
vp.type = Viewport.Type.Top
elif view == "Bottom":
vp.type = Viewport.Type.Bottom
elif view == "Front":
vp.type = Viewport.Type.Front
elif view == "Back":
vp.type = Viewport.Type.Back
elif view == "Left":
vp.type = Viewport.Type.Left
elif view == "Right":
vp.type = Viewport.Type.Right
vp.zoom_all()
vp.render_image(size=(800, 600),
filename=filename,
background=(0, 0, 0),
frame=0)
pipeline.remove_from_scene()
else:
print(
"Cannot use function ovito_view - the package ovito is not installed or cannot be found."
)