def write_config(sim, fields=None, precision=None):
"""
Write configurations to a trajectory file.
The trajectory format is taken from the passed Simulation
instance.
"""
# Initialize
# This will clear the variable in a new run
if sim.current_step == 0 or not hasattr(sim, '__init_write_config'):
sim.__init_write_config = False
if sim.restart:
sim.__init_write_config = True
# Header
if not sim.__init_write_config:
sim.__init_write_config = True
# TODO: folder-based trajectories should ensure that mode='w' clears up the folder
rmd(sim.output_path)
rmf(sim.output_path)
with sim.trajectory_class(sim.output_path, 'a') as t:
if precision is not None:
t.precision = precision
if fields is not None:
t.fields = fields
t.write(sim.system, sim.current_step)
def tearDown(self):
rmf(self.inpfile)
rmd(self.inpdir)
def tearDown(self):
rmf('/tmp/test_potential.h5')
def test_rm_glob(self):
utils.rmf(self.dirout + '/*')
self.assertFalse(os.path.exists(self.dirout + '/1'))
self.assertFalse(os.path.exists(self.dirout + '/2'))
self.assertTrue(os.path.exists(self.dirout + '/3'))
def test_rm(self):
utils.rmf([self.dirout + '/1', self.dirout + '/2'])
self.assertFalse(os.path.exists(self.dirout + '/1'))
self.assertFalse(os.path.exists(self.dirout + '/2'))
self.assertTrue(os.path.exists(self.dirout + '/3'))
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 tearDown(self):
from atooms.core.utils import rmf, rmd
rmf('/tmp/test_backends*')
rmd('/tmp/test_backends')
def tearDown(self):
rmd('/tmp/test_lammps.d')
rmf('/tmp/test_lammps*')
def tearDown(self):
from atooms.core.utils import rmf
rmf('/tmp/test_utils*')