def bilayer_lipid():
import matplotlib.pyplot as plt
outfile = "/home/mho/Downloads/new-self-ass.h5"
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
outfile, stride=10)
config = readdyviewer.Configuration()
t = readdy.Trajectory(outfile)
config.colors[t.particle_types['Head']] = readdyviewer.Color(
plt.cm.jet(0)[0],
plt.cm.jet(0)[1],
plt.cm.jet(0)[2])
config.radii[t.particle_types['Head']] = .7
config.colors[t.particle_types['Tail']] = readdyviewer.Color(
plt.cm.jet(1.)[0],
plt.cm.jet(1.)[1],
plt.cm.jet(1.)[2])
config.radii[t.particle_types['Tail']] = .7
config.stride = 1
config.smoothing = 5
config.cutoff = 5
config.bond_radius = .02
config.wait = 3
config.draw_periodic = True
config.set_box_size(25, 25, 25)
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config) #
def create_and_show_sim():
try:
import os
import readdy.util.io_utils as ioutils
import matplotlib.pyplot as plt
if os.path.exists('out.h5'):
os.unlink('out.h5')
system = readdy.ReactionDiffusionSystem([25., 25., 25.],
temperature=300. *
readdy.units.kelvin)
system.add_species("A", 1.0)
system.reactions.add("myfusion: A +(2) A -> A", rate=10.)
system.reactions.add("myfission: A -> A +(2) A", rate=3.)
system.potentials.add_harmonic_repulsion("A",
"A",
force_constant=10.,
interaction_distance=2.)
simulation = system.simulation(kernel="CPU")
simulation.output_file = "out.h5"
simulation.reaction_handler = "UncontrolledApproximation"
simulation.add_particle("A", [0., 0., 0.])
simulation.record_trajectory(stride=1)
simulation.observe.number_of_particles(stride=100)
simulation.run(n_steps=3000, timestep=1e-2)
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
simulation.output_file, stride=10)
config = readdyviewer.Configuration()
t = readdy.Trajectory(simulation.output_file)
config.colors[t.particle_types['A']] = readdyviewer.Color(
plt.cm.jet(0)[0],
plt.cm.jet(0)[1],
plt.cm.jet(0)[2])
config.radii[t.particle_types['A']] = 7
config.stride = 1
config.smoothing = 3
config.cutoff = 5
config.bond_radius = .02
config.wait = 5
config.clearcolor = readdyviewer.Color(.5, .5, .5)
config.draw_periodic = False
config.set_box_size(25, 25, 25)
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config)
finally:
if os.path.exists('out.h5'):
os.unlink('out.h5')
def edges():
print(readdyviewer.__file__)
trajfile = "/home/mho/Development/readdyviewer/tests/topology_simulation.h5"
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
trajfile)
config = readdyviewer.Configuration()
t = readdy.Trajectory(trajfile)
entries = t.read()
time, topology_records = t.read_observable_topologies()
print(len(topology_records))
print(len(topology_records[0][0].edges))
edges = []
for timestep, tops in zip(time, topology_records):
current_edges = []
for top in tops:
for e1, e2 in top.edges:
if e1 <= e2:
ix1 = top.particles[e1]
ix2 = top.particles[e2]
current_edges.append((ix1, ix2))
p1 = entries[timestep][ix1]
p2 = entries[timestep][ix2]
assert p1.type == 'T' or p1.type == 'unstable T', "expected topology type but got {} -- {}".format(
p1, p2)
assert p2.type == 'T' or p2.type == 'unstable T', "expected topology type but got {} -- {}".format(
p1, p2)
edges.append(current_edges)
config.colors[t.particle_types['unstable T']] = readdyviewer.Color(
153. / 255., 255. / 255., 0.)
config.radii[t.particle_types['unstable T']] = .5
config.colors[t.particle_types['T']] = readdyviewer.Color(
255. / 255., 153. / 255., 0.)
config.radii[t.particle_types['T']] = .5
config.colors[t.particle_types['Ligand']] = readdyviewer.Color(.5, .5, .5)
config.radii[t.particle_types['Ligand']] = 1.
config.colors[t.particle_types['Decay']] = readdyviewer.Color(.1, .2, .3)
config.radii[t.particle_types['Decay']] = .5
config.stride = 1
config.smoothing = 10
config.bond_radius = .2
config.cutoff = 3
config.edge_color = readdyviewer.Color(.1, .1, .1)
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config, edges)
def get_config_brighter(outfile):
import readdy.util.io_utils as ioutils
config = readdyviewer.Configuration()
p_types = ioutils.get_particle_types(outfile)
config.colors[p_types['ReaDDy_inactive']] = readdyviewer.Color(
0. / 255., 0. / 255., 0. / 255.)
config.radii[p_types['ReaDDy_inactive']] = 1.
config.colors[p_types['ReaDDy_active']] = readdyviewer.Color(
255. / 255., 50. / 255., 0. / 255.)
config.radii[p_types['ReaDDy_active']] = 1.2
config.colors[p_types['Activator']] = readdyviewer.Color(
200. / 255., 200. / 255., 255. / 255.)
config.radii[p_types['Activator']] = .9
config.colors[p_types['Activator_predator']] = readdyviewer.Color(
130. / 255., 170. / 255., 155. / 255.)
config.radii[p_types['Activator_predator']] = .4
config.stride = 1
config.clearcolor = readdyviewer.Color(15. / 255., 15. / 255., 15. / 255.)
return config
def test_cylinders():
n_particles_per_frame = np.array([2], dtype=int)
positions = np.array([[[2., -4., 1.], [0, 0., 0.]]])
types = np.array([[0, 0]], dtype=int)
ids = np.array([[0, 1]], dtype=int)
config = readdyviewer.Configuration()
config.colors[0] = readdyviewer.Color(153. / 255., 255. / 255., 0.)
config.radii[0] = .1
config.stride = 1
edges = [[(0, 1)]]
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config, edges)
def get_config_solarized_light(outfile):
import readdy.util.io_utils as ioutils
config = readdyviewer.Configuration()
p_types = ioutils.get_particle_types(outfile)
config.colors[p_types['ReaDDy_inactive']] = readdyviewer.Color(
128. / 255., 0. / 255., 0. / 255.)
config.radii[p_types['ReaDDy_inactive']] = 1.
config.colors[p_types['ReaDDy_active']] = readdyviewer.Color(
255. / 255., 50. / 255., 47. / 255.)
config.radii[p_types['ReaDDy_active']] = 1.2
config.colors[p_types['Activator']] = readdyviewer.Color(
139. / 255., 210. / 255., 255. / 255.)
config.radii[p_types['Activator']] = .9
config.colors[p_types['Activator_predator']] = readdyviewer.Color(
181. / 255., 137. / 255., 137. / 255.)
config.radii[p_types['Activator_predator']] = .4
config.stride = 1
config.clearcolor = readdyviewer.Color(
227. / 255., 227. / 255., 227. /
255.) # readdyviewer.Color(253. / 255., 246. / 255., 227. / 255.)
return config
def get_config_rgb_light_gray(outfile):
import readdy.util.io_utils as ioutils
config = readdyviewer.Configuration()
p_types = ioutils.get_particle_types(outfile)
config.colors[p_types['ReaDDy_inactive']] = readdyviewer.Color(
128. / 255., 0. / 255., 0. / 255.)
config.radii[p_types['ReaDDy_inactive']] = 1.
config.colors[p_types['ReaDDy_active']] = readdyviewer.Color(
230. / 255., 9. / 255., 9. / 255.)
config.radii[p_types['ReaDDy_active']] = 1.2
config.colors[p_types['Activator']] = readdyviewer.Color(
9. / 255., 230. / 255., 230. / 255.)
config.radii[p_types['Activator']] = .9
config.colors[p_types['Activator_predator']] = readdyviewer.Color(
120. / 255., 230. / 255., 9. / 255.)
config.radii[p_types['Activator_predator']] = .4
config.stride = 1
config.clearcolor = readdyviewer.Color(
240. / 255., 240. / 255., 240. /
255.) # readdyviewer.Color(253. / 255., 246. / 255., 227. / 255.)
return config
def more_topologies_sim():
trajfile = "/home/mho/Development/readdyviewer/tests/more_topologies_simulation.h5"
n_particles_per_frame, positions, types, ids = load_trajectory_to_npy(
trajfile)
config = readdyviewer.Configuration()
t = readdy.Trajectory(trajfile)
entries = t.read()
time, topology_records = t.read_observable_topologies()
edges = []
for timestep, tops in enumerate(topology_records):
current_edges = []
for top in tops:
for e1, e2 in top.edges:
ix1 = top.particles[e1]
ix2 = top.particles[e2]
current_edges.append((ix1, ix2))
p1 = entries[timestep][ix1]
p2 = entries[timestep][ix2]
assert p1.type == 'T' or p1.type == 'center T', "expected topology type but got {} -- {}".format(
p1, p2)
assert p2.type == 'T' or p2.type == 'center T', "expected topology type but got {} -- {}".format(
p1, p2)
edges.append(current_edges)
config.colors[t.particle_types['center T']] = readdyviewer.Color(
153. / 255., 255. / 255., 0.)
config.radii[t.particle_types['center T']] = .5
config.colors[t.particle_types['T']] = readdyviewer.Color(
255. / 255., 153. / 255., 0.)
config.radii[t.particle_types['T']] = .5
config.clearcolor = readdyviewer.Color(155. / 255., 155. / 255.,
155. / 255.)
config.stride = 1
print(positions.shape)
print("go!")
readdyviewer.watch_npy(positions, types, ids, n_particles_per_frame,
config, edges)