def open_mode(ascii_file, mode_index, supercell=[2,2,2], animate=True, n_frames=30, vectors=False, bbox=True, bbox_offset=(0,0,0), scale_factor=1.0, vib_magnitude=1.0, arrow_magnitude=1.0):
"""
Open v_sim ascii file in Blender
Arguments:
ascii_file: Path to file
mode_index: integer id of mode; 0 corresponds to first mode in ascii file
supercell: 3-tuple or list of integer supercell dimensions
animate: Boolean: if True, add animation keyframes
n_frames: Animation length in frames
vectors: Boolean; if True, show arrows
bbox: Boolean; if True, show bounding box
bbox_loc: Vector or 3-tuple in lattice vector coordinates; position of bbox. Default (0,0,0) (Left front bottom)
"""
vsim_cell, positions, symbols, vibs = import_vsim(ascii_file)
lattice_vectors = cell_vsim_to_vectors(vsim_cell)
# Switch to a new empty scene
bpy.ops.scene.new(type='EMPTY')
# Draw bounding box #
if bbox:
bbox_offset = Vector(bbox_offset)
draw_bounding_box(lattice_vectors, offset=bbox_offset)
# Draw atoms
for cell_id_tuple in itertools.product(range(supercell[0]),range(supercell[1]),range(supercell[2])):
cell_id = Vector(cell_id_tuple)
for atom_index, (position, symbol) in enumerate(zip(positions, symbols)):
atom = add_atom(position,lattice_vectors,symbol,cell_id=cell_id, name = '{0}_{1}_{2}{3}{4}'.format(atom_index,symbol,*cell_id_tuple), scale_factor=scale_factor)
displacement_vector = vibs[mode_index].vectors[atom_index]
qpt = vibs[mode_index].qpt
B = 2 * math.pi * Matrix(lattice_vectors).inverted().transposed()
qpt_cartesian = Vector(qpt) * B
if animate:
animate_atom_vibs(atom, qpt_cartesian, displacement_vector,
n_frames=n_frames, magnitude=vib_magnitude)
if vectors:
arrow_vector=vector_with_phase(atom, qpt_cartesian, displacement_vector)
add_arrow(loc=absolute_position(position, lattice_vectors=lattice_vectors,
cell_id=cell_id),
rot_euler=vector_to_euler(arrow_vector),
scale=arrow_vector.length*arrow_magnitude)
# Position camera and colour world
# Note that cameras as objects and cameras as 'cameras' have different attributes,
# so need to look up camera in bpy.data.cameras to set field of view.
field_of_view = 0.5 # Camera field of view in radians
camera_x = (lattice_vectors[0][0]/2. + lattice_vectors[2][0]/2.) * supercell[0]
camera_y = max(((abs(lattice_vectors[0][0]) + abs(lattice_vectors[2][0]) + 2) * supercell[0],
abs(lattice_vectors[2][2]) * supercell[2] + 2)) / (-2. * math.tan(field_of_view/2.))
camera_z = lattice_vectors[2][2]/2. * supercell[2]
camera_loc=( camera_x,
1.05 * camera_y,
camera_z)
bpy.ops.object.camera_add(location=camera_loc,rotation=(math.pi/2,0,0))
camera = bpy.context.object
bpy.context.scene.camera = camera
bpy.data.cameras[camera.name].angle = field_of_view
bpy.context.scene.world = bpy.data.worlds['World']
bpy.data.worlds['World'].horizon_color = [0.5, 0.5, 0.5]
def open_mode(**options):
"""
Open v_sim ascii file in Blender
:param input_file: Path to file
:type input_file: str
:param camera_rot: Camera tilt adjustment in degrees
:type camera_rot: float
:param config: Settings from configuration files
:type config: configparser.ConfigParser
:param mass_weighting: Weight eigenvectors by mass.
This has usually already been done when generating the .ascii file,
in which case the default value of 0 is acceptable.
A value of 1 corresponds to the formally correct mass scaling of m^-0.5
for non-weighted eigenvectors.
A value of -1 will REMOVE existing mass-weighting.
In-between values may be useful for re-scaling to see the range of
movements in a system, but are not physically meaningful.
:type mass_weighting: float
:param end_frame: The ending frame number of the rendered Animation
(default=start_frame+n_frames-1)
:type end_frame: int or None
:param miller: Miller indices of view
:type miller: 3-tuple of floats
:param mode_index: id of mode; 0 corresponds to first mode in ascii file
:type mode_index: int
:param n_frames: Animation length of a single oscillation
cycle in frames (default=30)
:type n_frames: Positive int
:param normalise_vectors: Re-scale vectors so largest arrow is fixed length
:type normalise_vectors: bool
:param offset_box: Position of bbox in lattice vector coordinates.
Default (0,0,0) (Left front bottom)
:type offset_box: Vector or 3-tuple
:param preview: Enable preview mode - single frame, smaller render
:type preview: bool
:param scale_arrow: Scale factor for arrows
:type scale_arrow: float
:param scale_atom: Scale of atoms, relative to covalent radius
:type scale_atom: float
:param scale_vib: Scale factor for oscillations
(angstroms / normalised eigenvector).
:type scale_vib: float
:param show_box: If True, show bounding box
:type show_box: bool
:param start_frame: The starting frame number of the rendered
animation (default=0)
:type start_frame: int or None
:param static: if True, ignore frame range and use single frame.
Otherwise, add animation keyframes.
:type static: bool
:param supercell: supercell dimensions
:type supercell: 3-tuple or 3-list of ints
:param vectors: If True, show arrows
:type vectors: bool
:param zoom: Camera zoom adjustment
:type zoom: float
"""
# Initialise Opts object, accessing options and user config
opts = vsim2blender.Opts(options)
# Work out actual frame range.
# Priority goes 1. static/preview 2. end_frame 3. n_frames
start_frame = opts.get('start_frame', 0)
n_frames = opts.get('n_frames', 30)
# Preview images default to static, others default to animated
preview = opts.get('preview', False)
if preview:
static = opts.get('static', True)
else:
static = opts.get('static', False)
if static:
end_frame = start_frame
else:
end_frame = opts.get('end_frame', start_frame + n_frames - 1)
input_file = opts.get('input_file', False)
if input_file:
(vsim_cell, positions, symbols, vibs) = import_vsim(input_file)
lattice_vectors = cell_vsim_to_vectors(vsim_cell)
else:
raise Exception('No .ascii file provided')
if opts.get('mass_weighting', 0):
f = opts.get('mass_weighting', 1)
masses = [
float(opts.config['masses'][symbol])**f for symbol in symbols
]
else:
masses = [1 for symbol in symbols]
# Switch to a new empty scene
bpy.ops.scene.new(type='EMPTY')
# Draw bounding box
if (opts.get('show_box', True)):
bbox_offset = opts.get('offset_box', (0, 0, 0))
bbox_offset = Vector(bbox_offset)
draw_bounding_box(lattice_vectors, offset=bbox_offset)
# Draw atoms after checking config
mode_index = opts.get('mode_index', 0)
supercell = (opts.get('supercell', (2, 2, 2)))
vectors = opts.get('vectors', False)
normalise_vectors = opts.get('normalise_vectors', False)
# Variable for tracking largest arrow
max_vector = 0
arrow_objects = []
mass_weighting = opts.get('mass_weighting', 0.)
assert type(mass_weighting) == float
for cell_id_tuple in itertools.product(range(supercell[0]),
range(supercell[1]),
range(supercell[2])):
cell_id = Vector(cell_id_tuple)
for (atom_index, (position, symbol,
mass)) in enumerate(zip(positions, symbols, masses)):
atom = add_atom(position,
lattice_vectors,
symbol,
cell_id=cell_id,
scale_factor=opts.get('scale_atom', 1.),
name='{0}_{1}_{2}{3}{4}'.format(
atom_index, symbol, *cell_id_tuple),
config=opts.config)
if vectors or not static:
displacement_vector = vibs[mode_index].vectors[atom_index]
qpt = vibs[mode_index].qpt
B = (2 * math.pi *
Matrix(lattice_vectors).inverted().transposed())
qpt_cartesian = Vector(qpt) * B
if not static:
animate_atom_vibs(atom,
qpt_cartesian,
displacement_vector,
start_frame=start_frame,
end_frame=end_frame,
n_frames=n_frames,
magnitude=opts.get('scale_vib', 1.),
mass=mass)
if vectors:
arrow_vector = vector_with_phase(atom, qpt_cartesian,
displacement_vector)
scale = arrow_vector.length
loc = absolute_position(position,
lattice_vectors=lattice_vectors,
cell_id=cell_id)
# Arrows are scaled by eigenvector magnitude
arrow_objects.append(
add_arrow(loc=loc,
mass=mass,
rot_euler=vector_to_euler(arrow_vector),
scale=scale))
if vectors:
col = str2list(opts.config.get('colours', 'arrow',
fallback='0. 0. 0.'))
bpy.data.materials['Arrow'].diffuse_color = col
# Rescaling; either by clamping max or accounting for cell size
if vectors and normalise_vectors:
master_scale = opts.get('scale_arrow', 1.)
# Compare first element of object scales; they should be isotropic!
max_length = max((arrow.scale[0] for arrow in arrow_objects))
for arrow in arrow_objects:
arrow.scale *= master_scale / max_length
elif vectors:
master_scale = opts.get('scale_arrow', 1.) * len(positions)
for arrow in arrow_objects:
arrow.scale *= master_scale
# Position camera and colour world. Note that cameras as objects and
# cameras as 'cameras' have different attributes, so need to look up
# camera in bpy.data.cameras to set field of view.
camera.setup_camera(lattice_vectors, field_of_view=0.2, opts=opts)
bpy.context.scene.world = bpy.data.worlds['World']
bpy.data.worlds['World'].horizon_color = str2list(
opts.config.get('colours', 'background', fallback='0.5 0.5 0.5'))
def open_mode(**options):
"""
Open v_sim ascii file in Blender
:param input_file: Path to file
:type input_file: str
:param camera_rot: Camera tilt adjustment in degrees
:type camera_rot: float
:param config: Settings from configuration files
:type config: configparser.ConfigParser
:param do_mass_weighting: Weight eigenvectors by mass.
This is not usually required.
:type do_mass_weighting: bool
:param end_frame: The ending frame number of the rendered Animation
(default=start_frame+n_frames-1)
:type end_frame: int or None
:param miller: Miller indices of view
:type miller: 3-tuple of floats
:param mode_index: id of mode; 0 corresponds to first mode in ascii file
:type mode_index: int
:param n_frames: Animation length of a single oscillation
cycle in frames (default=30)
:type n_frames: Positive int
:param normalise_vectors: Re-scale vectors so largest arrow is fixed length
:type normalise_vectors: bool
:param offset_box: Position of bbox in lattice vector coordinates.
Default (0,0,0) (Left front bottom)
:type offset_box: Vector or 3-tuple
:param preview: Enable preview mode - single frame, smaller render
:type preview: bool
:param scale_arrow: Scale factor for arrows
:type scale_arrow: float
:param scale_atom: Scale of atoms, relative to covalent radius
:type scale_atom: float
:param scale_vib: Scale factor for oscillations
(angstroms / normalised eigenvector).
:type scale_vib: float
:param show_box: If True, show bounding box
:type show_box: bool
:param start_frame: The starting frame number of the rendered
animation (default=0)
:type start_frame: int or None
:param static: if True, ignore frame range and use single frame.
Otherwise, add animation keyframes.
:type static: bool
:param supercell: supercell dimensions
:type supercell: 3-tuple or 3-list of ints
:param vectors: If True, show arrows
:type vectors: bool
:param zoom: Camera zoom adjustment
:type zoom: float
"""
# Initialise Opts object, accessing options and user config
opts = vsim2blender.Opts(options)
# Work out actual frame range.
# Priority goes 1. static/preview 2. end_frame 3. n_frames
start_frame = opts.get('start_frame', 0)
n_frames = opts.get('n_frames', 30)
# Preview images default to static, others default to animated
preview = opts.get('preview', False)
if preview:
static = opts.get('static', True)
else:
static = opts.get('static', False)
if static:
end_frame = start_frame
else:
end_frame = opts.get('end_frame', start_frame + n_frames - 1)
input_file = opts.get('input_file', False)
if input_file:
(vsim_cell, positions, symbols, vibs) = import_vsim(input_file)
lattice_vectors = cell_vsim_to_vectors(vsim_cell)
else:
raise Exception('No .ascii file provided')
if opts.get('do_mass_weighting', False):
masses = [float(opts.config['masses'][symbol]) for symbol in symbols]
else:
masses = [1 for symbol in symbols]
# Switch to a new empty scene
bpy.ops.scene.new(type='EMPTY')
# Draw bounding box
if (opts.get('show_box', True)):
bbox_offset = opts.get('offset_box', (0, 0, 0))
bbox_offset = Vector(bbox_offset)
draw_bounding_box(lattice_vectors, offset=bbox_offset)
# Draw atoms after checking config
mode_index = opts.get('mode_index', 0)
supercell = (opts.get('supercell', (2, 2, 2)))
vectors = opts.get('vectors', False)
normalise_vectors = opts.get('normalise_vectors', False)
# Variable for tracking largest arrow
max_vector = 0
arrow_objects = []
for cell_id_tuple in itertools.product(range(supercell[0]),
range(supercell[1]),
range(supercell[2])):
cell_id = Vector(cell_id_tuple)
for (atom_index,
(position, symbol, mass)) in enumerate(zip(positions,
symbols,
masses)):
atom = add_atom(position, lattice_vectors, symbol,
cell_id=cell_id,
name='{0}_{1}_{2}{3}{4}'.format(
atom_index, symbol, *cell_id_tuple),
config=opts.config)
if vectors or not static:
displacement_vector = vibs[mode_index].vectors[atom_index]
qpt = vibs[mode_index].qpt
B = (2 * math.pi *
Matrix(lattice_vectors).inverted().transposed())
qpt_cartesian = Vector(qpt) * B
if not static:
animate_atom_vibs(atom, qpt_cartesian,
displacement_vector,
start_frame=start_frame,
end_frame=end_frame,
n_frames=n_frames,
magnitude=opts.get('scale_vib', 1.),
mass=mass)
if vectors:
arrow_vector = vector_with_phase(atom, qpt_cartesian,
displacement_vector)
max_vector = max(max_vector, arrow_vector.length)
loc = absolute_position(position,
lattice_vectors=lattice_vectors,
cell_id=cell_id)
# Arrows are scaled by eigenvector magnitude
arrow_objects.append(
add_arrow(loc=loc,
mass=mass,
rot_euler=vector_to_euler(arrow_vector),
scale=arrow_vector.length))
if vectors:
col = str2list(opts.config.get('colours', 'arrow',
fallback='0. 0. 0.'))
bpy.data.materials['Arrow'].diffuse_color = col
# Rescaling; either by clamping max or accounting for cell size
if vectors and normalise_vectors:
scale = opts.get('scale_arrow', 1.) / max_vector
for arrow in arrow_objects:
arrow.scale *= scale
elif vectors:
scale = opts.get('scale_arrow', 1.) * len(positions)
for arrow in arrow_objects:
arrow.scale *= scale
# Position camera and colour world. Note that cameras as objects and
# cameras as 'cameras' have different attributes, so need to look up
# camera in bpy.data.cameras to set field of view.
camera.setup_camera(lattice_vectors, field_of_view=0.2, opts=opts)
bpy.context.scene.world = bpy.data.worlds['World']
bpy.data.worlds['World'].horizon_color = str2list(opts.config.get(
'colours', 'background', fallback='0.5 0.5 0.5'))