"""
ZnVis: A Zincwarecode package.
License
-------
This program and the accompanying materials are made available under the terms
of the Eclipse Public License v2.0 which accompanies this distribution, and is
available at https://www.eclipse.org/legal/epl-v20.html
SPDX-License-Identifier: EPL-2.0
Copyright Contributors to the Zincwarecode Project.
Contact Information
-------------------
email: zincwarecode@gmail.com
github: https://github.com/zincware
web: https://zincwarecode.com/
Citation
--------
If you use this module please cite us with:
Summary
-------
Module for the particle parent class
"""
import typing
from dataclasses import dataclass
import numpy as np
from rich.progress import track
from znvis.mesh import Mesh
[docs]@dataclass
class Particle:
"""
Parent class for a ZnVis particle.
Attributes
----------
name : str
Name of the particle
mesh : Mesh
Mesh to use e.g. sphere
position : np.ndarray
Position tensor of the shape (n_confs, n_particles, n_dims)
velocity : np.ndarray
Velocity tensor of the shape (n_confs, n_particles, n_dims)
force : np.ndarray
Force tensor of the shape (n_confs, n_particles, n_dims)
director: np.ndarray
Director tensor of the shape (n_confs, n_particles, n_dims)
mesh_list : list
A list of mesh objects, one for each time step.
smoothing : bool (default=False)
If true, apply smoothing to each mesh object as it is rendered.
This will slow down the initial construction of the mesh objects
but not the deployment.
"""
name: str
mesh: Mesh = None
position: np.ndarray = None
velocity: np.ndarray = None
force: np.ndarray = None
director: np.ndarray = None
mesh_list: typing.List[Mesh] = None
smoothing: bool = False
def _create_mesh(self, position, director):
"""
Create a mesh object for the particle.
Parameters
----------
position : np.ndarray
Position of the particle
director : np.ndarray
Director of the particle
Returns
-------
mesh : o3d.geometry.TriangleMesh
A mesh object
"""
if director is not None:
mesh = self.mesh.create_mesh(position, starting_orientation=director)
else:
mesh = self.mesh.create_mesh(position)
if self.smoothing:
return mesh.filter_smooth_taubin(100)
else:
return mesh
[docs] def construct_mesh_list(self):
"""
Constructor the mesh list for the class.
The mesh list is a list of mesh objects for each
time step in the parsed trajectory.
Returns
-------
Updates the class attributes mesh_list
"""
self.mesh_list = []
try:
n_particles = int(self.position.shape[1])
n_time_steps = int(self.position.shape[0])
except ValueError:
raise ValueError("There is no data for these particles.")
for i in track(range(n_time_steps), description=f"Building {self.name} Mesh"):
for j in range(n_particles):
if j == 0:
if self.director is not None:
mesh = self._create_mesh(
self.position[i][j], self.director[i][j]
)
else:
mesh = self._create_mesh(self.position[i][j], None)
else:
if self.director is not None:
mesh += self._create_mesh(
self.position[i][j], self.director[i][j]
)
else:
mesh += self._create_mesh(self.position[i][j], None)
self.mesh_list.append(mesh)