[docs]def planar_sheet():
"""
Specification for a 2D sheet in the plane
"""
spec = {
"edge": {
"trgt": 0,
"nz": 1.0,
"length": 1.0,
"face": 0,
"srce": 0,
"dx": 0.0,
"dy": 0.0,
"sx": 0.0,
"sy": 0.0,
"tx": 0.0,
"ty": 0.0,
"fx": 0.0,
"fy": 0.0,
},
"vert": {"y": 0.0, "is_active": 1, "x": 0.0},
"face": {
"y": 0.0,
"is_alive": 1,
"perimeter": 0.0,
"area": 0.0,
"x": 0.0,
"num_sides": 6,
"id": 0,
},
"settings": {"geometry": "planar"},
}
return spec
[docs]def planar_spec():
return planar_sheet()
[docs]def planar_periodic_sheet():
spec = planar_sheet()
spec["settings"] = {"boundaries": {"x": [-1, 1], "y": [-1, 1]}}
return spec
[docs]def sheet_spec():
spec = {
"face": {
"x": 0.0,
"y": 0.0,
"z": 0.0,
"num_sides": 6,
"area": 1.0,
"perimeter": 1.0,
"is_alive": 1,
"id": 0,
},
"vert": {
"x": 0.0,
"y": 0.0,
"z": 0.0,
"is_active": 1,
"rho": 0.0,
"height": 0.0,
"basal_shift": 4.0,
},
"edge": {
"srce": 0,
"trgt": 0,
"face": 0,
"dx": 0.0,
"dy": 0.0,
"dz": 0.0,
"nx": 0.0,
"ny": 0.0,
"nz": 1.0,
"sx": 0.0,
"sy": 0.0,
"sz": 0.0,
"tx": 0.0,
"ty": 0.0,
"tz": 0.0,
"fx": 0.0,
"fy": 0.0,
"fz": 0.0,
"length": 1.0,
"is_active": 1,
},
"settings": {"geometry": "cylindrical", "height_axis": "z"},
}
return spec
[docs]def periodic_sheet():
spec = planar_sheet()
spec["settings"].update({"boundaries": {"x": [-1, 1], "y": [-1, 1]}})
return spec
[docs]def cylindrical_sheet():
"""Geometry specification of a sheet in a 3D space."""
spec = sheet_spec()
return spec
[docs]def rod_sheet():
"""Geomtetry specs of a rod sheet in 3D space."""
spec = sheet_spec()
spec["settings"].update({"geometry": "rod", "height_axis": "z", "ab": [0.0, 0.0]})
spec["vert"].update({"left_tip": False, "right_tip": False})
return spec
[docs]def flat_sheet():
"""Geometry specification of a sheet in a 3D space."""
spec = sheet_spec()
spec["settings"].update({"geometry": "flat"})
return spec
[docs]def spherical_sheet():
"""Geometry specification of a sheet in a 3D space.
Height is computed with respect to the distance to
the coordinate systems center
"""
spec = sheet_spec()
spec["settings"].update({"geometry": "spherical"})
return spec
[docs]def bulk_spec():
"""Geometry specification for bulk tissues."""
spec = sheet_spec()
spec["edge"].update({"cx": 0.0, "cy": 0.0, "cz": 0.0, "cell": 0, "sub_vol": 0.0})
spec["cell"] = {
"x": 0.0,
"y": 0.0,
"z": 0.0,
"area": 0.0,
"vol": 0.0,
"num_faces": 6,
"is_alive": 1,
"id": 0,
}
return spec
