Visualizing GSD File

In this example, we will use fresnel to visualize a gsd file. We will color the particles & bonds by types, as well as visualize the simulation box.

We will need the gsd package to run this example.

import fresnel
import gsd.hoomd
import numpy as np

First we read in the .gsd file.

with gsd.hoomd.open(name="molecules.gsd", mode="rb") as gsd_file:
    snap = gsd_file[0]

box = snap.configuration.box

We want to color by particle type. We will color A types red, B types blue, and C types green.

N = snap.particles.N
particle_types = snap.particles.typeid
colors = np.empty((N, 3))

# Color by typeid
colors[particle_types == 0] = fresnel.color.linear([.95, 0, 0]) # A type
colors[particle_types == 1] = fresnel.color.linear([0, .95, 0]) # B type
colors[particle_types == 2] = fresnel.color.linear([0, 0, .95]) # C type

scene = fresnel.Scene()

# Spheres for every particle in the system
geometry = fresnel.geometry.Sphere(scene, N=N, radius=0.2)
geometry.position[:] = snap.particles.position
geometry.material = fresnel.material.Material(roughness=0.9)
geometry.outline_width = 0.05



# use color instead of material.color
geometry.material.primitive_color_mix = 1.0
geometry.color[:] = fresnel.color.linear(colors)

# create box in fresnel
fresnel.geometry.Box(scene, box, box_radius=.07)

<fresnel.geometry.Box at 0x7f5fbcb92670>

We will visualize bonds using cylinders, and color the bonds to match the particle types. To aid visualization, we will first remove any bonds that span the periodic boundary.

all_bonds = np.stack(
    [
        snap.particles.position[snap.bonds.group[:, 0]],
        snap.particles.position[snap.bonds.group[:, 1]],
    ],
    axis=1,
)

# Use a distance cutoff (L/2) to filter bonds that span the periodic boundary
bond_distances = np.linalg.norm(all_bonds[:,0,:]-all_bonds[:,1,:], axis=1)

# This simple method will work for cubic cells
L = box[0]
bond_indices = np.where(bond_distances < L/2)[0]
filtered_bonds = all_bonds[bond_indices, :, :]

N_bonds = filtered_bonds.shape[0]
bonds = fresnel.geometry.Cylinder(scene, N=N_bonds)
bonds.material = fresnel.material.Material(roughness=0.5)
bonds.outline_width = 0.05



# Color by bond typeid
bond_ids = snap.bonds.typeid[bond_indices]
bond_colors = np.empty((N_bonds, 3))
bond_colors[bond_ids == 0] = fresnel.color.linear([0, .95, 0])  # B-B Bonds
bond_colors[bond_ids == 1] = fresnel.color.linear([0, 0, .95])  # C-C Bonds

bonds.material.primitive_color_mix = 1.0
bonds.points[:] = filtered_bonds

bonds.color[:] = np.stack(
    [fresnel.color.linear(bond_colors), fresnel.color.linear(bond_colors)], axis=1
)
bonds.radius[:] = [0.1] * N_bonds

Now that we have everything setup, we will render everything and apply some ring lighting conditions.

scene.camera = fresnel.camera.Orthographic.fit(scene)
scene.lights = fresnel.light.lightbox()
fresnel.pathtrace(scene, light_samples=5)