def viewpoint(self, ):
view_str = ''
com = self._atoms.get_center_of_mass()
positions = self._atoms.positions
R = max(
max(positions[:, 0]) - min(positions[:, 0]),
max(positions[:, 1]) - min(positions[:, 1]))
camera_persp = build_tag('Viewpoint',
id="camera_persp_%s" % self.uuid,
position=tuple(com + [0, 0, 3 * R]),
centerOfRotation=tuple(com),
orientation="0 0 0 0",
description="camera")
camera_persp = build_tag('Transform',
id="t_camera_persp_%s" % self.uuid,
rotation='0 0 0 0',
body=camera_persp)
camera_ortho = build_tag('OrthoViewpoint',
id="camera_ortho_%s" % self.uuid,
position=tuple(com + [0, 0, 3 * R]),
centerOfRotation=tuple(com),
orientation="0 0 0 0",
fieldOfView='-{0} -{0} {0} {0}'.format(R),
description="camera")
camera_ortho = build_tag('Transform',
id="t_camera_ortho_%s" % self.uuid,
rotation='0 0 0 0',
body=camera_ortho)
view_str = camera_persp + camera_ortho
return view_str
def write(self, filename, datatype=None, **kwargs):
"""
"""
script = build_script(self.uuid, self.data)
body = build_html(self.uuid)
out, tail, datatype = write_header_tail(script, body, datatype,
filename)
#
view_str = self.viewpoint()
atomic_str = self.draw_atoms()
cell_str = self.draw_cells()
bond_str = self.draw_bonds()
polyhedra_str = self.draw_polyhedras()
iso_str = self.get_isosurface()
marker_str = self.draw_marker()
# animate
ani_str = self.animate()
scene_str = view_str + atomic_str + cell_str + bond_str + polyhedra_str + iso_str + marker_str + ani_str
scene_str = build_tag('Scene', body=scene_str)
if datatype == 'X3DOM':
x3d_str = build_tag('X3D',
id="x3dase",
PrimitiveQuality=self.quality,
body=scene_str)
x3d_str = build_tag('div',
dict={'class': 'column right'},
body=x3d_str)
elif datatype == 'X3D':
x3d_str = build_tag(
'X3D',
body=scene_str,
profile='Immersive',
version='3.0',
dict={
'xmlns:xsd':
'http://www.w3.org/2001/XMLSchema-instance',
'xsd:noNamespaceSchemaLocation':
' http://www.web3d.org/specifications/x3d-3.0.xsd'
})
out.extend(x3d_str)
out.extend(tail)
if isinstance(filename, str):
with open(filename, 'w') as f:
for line in out:
f.write(line)
else:
f = filename
for line in out:
f.write(''.join(line))
def draw_cells(self, celllinewidth=0.05):
"""
Draw unit cell
"""
cell_str = []
if self.cell_vertices is not None:
# edges
coordIndex = '0 1 -1 0 2 -1 0 4 -1 1 3 -1 1 5 -1 2 3 -1 2 6 -1 3 7 -1 4 5 -1 4 6 -1 5 7 -1 6 7 -1'
# coordIndex = '0 1 2 3 0 -1 4 5 6 7 4 -1 0 4 -1 1 5 -1 2 6 -1 3 7'
point = str(self.cell_vertices)
# edge
material = build_tag('Material',
diffuseColor=(0, 0, 0),
emissiveColor=(0, 0.5, 1))
appearance = build_tag('Appearance', body=material)
coord = build_tag('Coordinate', point=point)
edge = build_tag('IndexedLineSet',
coordIndex=coordIndex,
body=coord)
edge = build_tag('Shape', body=edge + appearance)
cell_str.extend(edge)
return cell_str
def animate(self, ):
'''
<timeSensor DEF="time" cycleInterval="2" loop="true"> </timeSensor>
<PositionInterpolator DEF="move" key="0 0.5 1" keyValue="0 0 0 0 3 0 0 0 0"> </PositionInterpolator>
<Route fromNode="time" fromField ="fraction_changed" toNode="move" toField="set_fraction> </Route>
<Route fromNode="move" fromField ="value_changed" toNode="ball" toField="translation> </Route>
'''
ani_str = []
if self.nimage == 1: return ani_str
ani_str.extend(
build_tag('TimeSensor',
DEF='time',
cycleInterval=self.nimage,
loop='true'))
for i in range(len(self._atoms)):
route1 = build_tag('ROUTE',
fromNode='time',
fromField='fraction_changed',
toNode='move_%s' % i,
toField='set_fraction')
route2 = build_tag('ROUTE',
fromNode="move_%s" % i,
fromField="value_changed",
toNode="at_%s_%s" % (i, self.uuid),
toField="translation")
key = ""
keyvalue = ""
for j in range(self.nimage):
key += " %s" % (j / self.nimage)
keyvalue += '%s %s %s ' % tuple(self.images[j][i].position)
pi = build_tag('PositionInterpolator',
DEF='move_%s' % i,
key=key,
keyValue=keyvalue)
ani_str.extend(pi)
ani_str.extend(route1)
ani_str.extend(route2)
return ani_str
def draw_bonds(self):
'''
Draw atom bonds
'''
# build materials
bond_str = []
if not self.bond:
return bond_str
bondlist = get_bondpairs(self._atoms,
cutoff=self.bond,
rmbonds=self.rmbonds)
self.bond_kinds = get_bond_kinds(self._atoms, self.atom_kinds,
bondlist)
group = []
for kind, datas in self.bond_kinds.items():
material = build_tag('Material', **datas['material'])
sphere = build_tag('Cylinder',
height=1.0,
radius=0.1,
subdivision=8)
appearance = build_tag('Appearance', body=material)
shape = build_tag('Shape', DEF=kind, body=appearance + sphere)
switch = build_tag('Switch', body=shape, whichChoice="-1")
bond_str.extend(switch)
for pos, height, rotation in zip(datas['centers'],
datas['lengths'],
datas['rotations']):
shape1 = build_tag('Shape', USE=kind)
bt = build_tag('Transform',
body=shape1,
translation=tuple(pos),
scale=(1, height, 1),
rotation=tuple(rotation))
group.extend(bt)
group = build_tag('Group', body=group)
bond_str.extend(
build_tag('Switch',
id="bs_%s" % self.uuid,
body=group,
whichChoice="-1"))
return bond_str
def draw_isosurface(self, vertices, faces, color):
"""
"""
iso_str = []
material = build_tag('Material', diffuseColor=color, transparency=0.4)
appearance = build_tag('Appearance', body=material)
facecoordIndex_str = ' '
coordinate_str = ' '
for face in faces:
facecoordIndex_str += ' '.join(str(x) for x in face) + ' -1 '
for coordinate in vertices:
coordinate_str += ' '.join(str(x) for x in coordinate) + ' '
coord = build_tag('Coordinate', point=coordinate_str)
face = build_tag('IndexedFaceSet',
solid='false',
coordIndex=facecoordIndex_str,
body=coord)
face = build_tag('Shape', body=face + appearance)
iso_str.extend(face)
iso_str = build_tag('Group',
onclick="handleGroupClick(event)",
body=iso_str)
return iso_str
def draw_polyhedras(self, ):
'''
Draw polyhedras
'''
polyhedra_str = []
if not self.polyhedra:
return polyhedra_str
bondlist = get_bondpairs(self._atoms,
cutoff=self.bond,
rmbonds=self.rmbonds)
self.polyhedra_kinds = get_polyhedra_kinds(self._atoms,
bondlist=bondlist,
polyhedra=self.polyhedra)
for kind, datas in self.polyhedra_kinds.items():
material = build_tag('Material',
**datas['material'],
ambientIntensity=0)
appearance = build_tag('Appearance', body=material)
facecoordIndex_str = ' '
coordinate_str = ' '
edgecoordIndex_str = ' '
for face in datas['faces']:
facecoordIndex_str += ' '.join(str(x) for x in face) + ' -1 '
for coordinate in datas['vertices']:
coordinate_str += ' '.join(str(x) for x in coordinate) + ' '
for edge in datas['edges']:
edgecoordIndex_str += ' '.join(str(x) for x in edge) + ' -1 '
coord = build_tag('Coordinate', point=coordinate_str)
# face
face = build_tag('IndexedFaceSet',
solid='false',
coordIndex=facecoordIndex_str,
body=coord)
polyhedra_str.extend(build_tag('Shape', body=face + appearance))
# edge
material = build_tag('Material',
diffuseColor=(1, 1, 1),
emissiveColor=(0.8, 0.8, 0.8),
ambientIntensity=0)
appearance = build_tag('Appearance', body=material)
edge = build_tag('IndexedLineSet',
coordIndex=edgecoordIndex_str,
body=coord)
polyhedra_str.extend(build_tag('Shape', body=edge + appearance))
polyhedra_str = build_tag('Group', body=polyhedra_str)
polyhedra_str = (build_tag('Switch',
id="ps_%s" % self.uuid,
body=polyhedra_str,
whichChoice="-1"))
return polyhedra_str
def draw_atoms(self):
'''
Draw atoms
bsdf_inputs: dict
The key and value for principled_bsdf node
material_style: string
Select materials type from ['blase', 'glass', 'ceramic', 'plastic'].
'''
# build materials
atomic_str = []
label_str = []
group_ele = []
group_ind = []
for kind, datas in self.atom_kinds.items():
material0 = build_tag('Material',
name='am_%s' % self.uuid,
**datas['material'])
sphere0 = build_tag('Sphere',
DEF='asp_%s' % kind,
**datas['sphere'])
appearance0 = build_tag('Appearance',
DEF='app_%s' % kind,
body=material0)
shape0 = build_tag('Shape',
DEF='as_%s' % kind,
id='as_%s_%s' % (kind, self.uuid),
body=appearance0 + sphere0)
atomic_str.extend(
build_tag('Switch', body=shape0, whichChoice="-1"))
# switch = build_tag('Switch', body = shape, whichChoice = "-1")
material1 = build_tag('Material', diffuseColor=(0, 0, 0))
appearance_text0 = build_tag('Appearance',
DEF='text_app_%s' % kind,
body=material1)
fontstyle0 = build_tag('Fontstyle',
DEF='st_label',
family="SANS",
size="%s" %
(datas['sphere']['radius'] /
2.0)) #, justify='"MIDDLE", "MIDDLE"')
label_str.extend(fontstyle0)
label_str.extend(appearance_text0)
# label_str.extend(switch)
# element text
ele = build_tag('Text', string=kind, solid='true', body=fontstyle0)
shape_ele0 = build_tag('Shape',
DEF=kind,
id='as_%s' % self.uuid,
body=appearance_text0 + ele)
shape_ele0 = build_tag('Billboard',
DEF='billboard_%s' % kind,
axisOfRotation=(0, 0, 0),
body=shape_ele0)
label_str.extend(
build_tag('Switch', body=shape_ele0, whichChoice="-1"))
iatom = 0
for pos in datas['positions']:
# atoms sphere
sphere = build_tag('Sphere', USE='asp_%s' % kind)
appearance = build_tag('Appearance', USE='app_%s' % kind)
shape = build_tag('Shape',
kind=kind,
index=datas['indexs'][iatom],
uuid=self.uuid,
body=appearance + sphere)
atomic_str.extend(
build_tag(
'Transform',
DEF="at_%s_%s" % (datas['indexs'][iatom], self.uuid),
uuid=self.uuid,
id="at_%s_%s" % (datas['indexs'][iatom], self.uuid),
radius=datas['sphere']['radius'],
name="at_%s" % (self.uuid),
body=shape,
translation=tuple(pos),
scale="1 1 1"))
# index
appearance = build_tag('Appearance', USE='text_app_%s' %
kind) #, justify='"MIDDLE", "MIDDLE"')
ind = build_tag('Text',
string=datas['indexs'][iatom],
solid='true',
body=fontstyle0)
shape_ind = build_tag('Shape', body=appearance + ind)
shape_ind = build_tag('Billboard',
axisOfRotation=(0, 0, 0),
body=shape_ind)
group_ind.extend(
build_tag('Transform',
body=shape_ind,
translation=tuple(pos)))
# element text
shape_ele = build_tag('Billboard',
axisOfRotation=(0, 0, 0),
USE='billboard_%s' % kind)
group_ele.extend(
build_tag('Transform',
body=shape_ele,
translation=tuple(pos)))
iatom += 1
atomic_str = build_tag('Group',
body=atomic_str,
onclick="handleGroupClick(event, '%s')" %
self.uuid)
if self.label:
group_ele = build_tag('Group', body=group_ele)
group_ind = build_tag('Group', body=group_ind)
atomic_str.extend(label_str)
atomic_str.extend(
build_tag('Switch',
id="ele_%s" % self.uuid,
body=group_ele,
whichChoice="-1"))
atomic_str.extend(
build_tag('Switch',
id="ind_%s" % self.uuid,
body=group_ind,
whichChoice="-1"))
return atomic_str
def draw_marker(self, ):
marker_str = []
# sphere
for i in range(5):
material = build_tag('Material',
diffuseColor="#FFD966",
transparency=0.5)
appearance = build_tag('Appearance', body=material)
sphere = build_tag('Sphere', radius=1.0)
shape = build_tag('Shape',
isPickable=False,
body=appearance + sphere)
trans = build_tag('Transform',
id='marker_%s_%s' % (i, self.uuid),
body=shape,
scale=".1 .1 .1",
translation="5 0 0")
marker_str.extend(
build_tag('Switch',
id='switch_marker_%s_%s' % (i, self.uuid),
body=trans,
whichChoice="-1"))
# lines
for i in range(2):
coordIndex = '0 1 -1'
point = '0 0 0 0 0 1'
material = build_tag('Material',
diffuseColor=(0, 0, 0),
emissiveColor=(0, 0.5, 1))
appearance = build_tag('Appearance', body=material)
coord = build_tag('Coordinate',
id='line_coor_%s_%s' % (i, self.uuid),
point=point)
line = build_tag('IndexedLineSet',
id='line_ind_%s_%s' % (i, self.uuid),
solid='false',
coordIndex=coordIndex,
body=coord)
line = build_tag('Shape', body=line + appearance)
marker_str.extend(
build_tag('Switch',
id='switch_line_%s_%s' % (i, self.uuid),
body=line,
whichChoice="-1"))
return marker_str