Visualization with plato

In this notebook, we run a Lennard-Jones simulation, color particles according to their local density computed with freud, and display the results with plato. Note that plato has multiple backends – see the plato documentation for information about each backend and the features it supports.

import hoomd
import hoomd.md
hoomd.context.initialize('')

# Silence the HOOMD output
hoomd.util.quiet_status()
hoomd.option.set_notice_level(0)

# Create a 10x10x10 simple cubic lattice of particles with type name A
system = hoomd.init.create_lattice(unitcell=hoomd.lattice.sc(a=1.5, type_name='A'), n=10)

# Specify Lennard-Jones interactions between particle pairs
nl = hoomd.md.nlist.cell()
lj = hoomd.md.pair.lj(r_cut=3.0, nlist=nl)
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0)

# Integrate at constant temperature
hoomd.md.integrate.mode_standard(dt=0.005)
integrator = hoomd.md.integrate.nvt(group=hoomd.group.all(), kT=0.01, tau=0.5)
integrator.randomize_velocities(seed=42)

# Run for 10,000 time steps
hoomd.run(10e3)
snap = system.take_snapshot()

HOOMD-blue v2.6.0-151-gea140cffb DOUBLE HPMC_MIXED MPI TBB SSE SSE2 SSE3 SSE4_1 SSE4_2 AVX AVX2
Compiled: 09/25/2019
Copyright (c) 2009-2019 The Regents of the University of Michigan.
-----
You are using HOOMD-blue. Please cite the following:
* J A Anderson, C D Lorenz, and A Travesset. "General purpose molecular dynamics
  simulations fully implemented on graphics processing units", Journal of
  Computational Physics 227 (2008) 5342--5359
* J Glaser, T D Nguyen, J A Anderson, P Liu, F Spiga, J A Millan, D C Morse, and
  S C Glotzer. "Strong scaling of general-purpose molecular dynamics simulations
  on GPUs", Computer Physics Communications 192 (2015) 97--107
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HOOMD-blue is running on the CPU

Now we import the modules needed for visualization.

import freud
import matplotlib.cm
from matplotlib.colors import Normalize
import numpy as np
import plato
# For interactive scenes, use:
import plato.draw.pythreejs as draw
# For static scenes, use:
#import plato.draw.fresnel as draw

This code sets up the plato Scene object with the particles and colors computed above.

positions = snap.particles.position
box = freud.Box.from_box(snap.box)
ld = freud.density.LocalDensity(3.0, 1.0)
ld.compute(system=snap)
colors = matplotlib.cm.viridis(Normalize()(ld.density))
radii = np.ones(len(positions)) * 0.5
box_prim = draw.Box.from_box(box, width=0.2)
sphere_prim = draw.Spheres(
    positions=snap.particles.position,
    radii=radii,
    colors=colors,
    vertex_count=32)
scene = draw.Scene((sphere_prim, box_prim), zoom=1.5)

Click and drag the 3D scene below - it’s interactive!

scene.show()