def test_4atoms():
a = Atom("Ar", [0.5, 0.5, 0])
b = Atom("Ar", [0.5, -0.5, 0])
c = Atom("Ar", [-0.2, -0.5, 0])
d = Atom("Ar", [-0.5, 0.5, 0.5])
sys = MonatomicSystem([a, b, c, d], 6.0)
v = Viewer()
sr = v.add_renderer(SphereRenderer, sys.atoms)
v.add_renderer(CubeRenderer, sys.boxsize)
# evo takes times in picoseconds
evo = evolve_generator(sys, t=1e3, tstep=0.002, periodic=True)
def update_pos():
try:
for i in range(100):
sys, t = evo.next()
sr.update(sys.r_array)
except StopIteration:
pass
#import pylab as pl
#pl.plot(distances, pitentials, 'o')
#pl.show()
v.schedule(update_pos)
v.run()
def test_3():
'''Make this much more interactive'''
from chemlab.graphics.processviewer import ProcessViewer
boxsize = 30.0
nmol = 1000
sys = MonatomicSystem.random("Ar", nmol, boxsize)
v = ProcessViewer()
pr = v.add_renderer(SphereRenderer, sys.atoms)
v.add_renderer(CubeRenderer, boxsize)
for i in range(100):
# Let's try to make periodic boundary conditions
farray = forces.lennard_jones(sys.r_array, "Ar", periodic=boxsize)
# Just this time let's assume masses are 1
sys.r_array, sys.varray = integrators.euler(sys.r_array, sys.varray, farray/30.17, 0.01)
# Add more periodic conditions
rarray = sys.r_array
i_toopositive = rarray > boxsize * 0.5
rarray[i_toopositive] -= boxsize
i_toonegative = rarray < - boxsize * 0.5
rarray[i_toonegative] += boxsize
sys.r_array = rarray
pr.update(rarray)
v._p.join()
def test_periodic():
'''Now let's try to implement the periodic boundaries, we should
try to put the molecules near the border and see if one molecule
'passes' the wall.
'''
import pyglet
pyglet.options['vsync'] = False
# Let's say we have to store this in nm and picoseconds
# I setup argon atoms pretty overlapping
a = Atom("Ar", [0.5, 0.0, 0.0])
b = Atom("Ar", [-1.4, 0.0, 0.0])
sys = MonatomicSystem([a, b], 3.0)
v = Viewer()
sr = v.add_renderer(SphereRenderer, sys.atoms)
v.add_renderer(CubeRenderer, sys.boxsize)
# evo takes times in picoseconds
evo = evolve_generator(sys, t=1e3, tstep=0.002, periodic=True)
distances = [np.linalg.norm(sys.r_array[0] - sys.r_array[1])]
pitentials = [
cenergy.lennard_jones(sys.r_array * 1e-9, 'Ar', periodic=False)
]
def update_pos():
try:
for i in range(100):
sys, t = evo.next()
dist = np.linalg.norm(sys.r_array[0] - sys.r_array[1])
pot = cenergy.lennard_jones(sys.r_array * 1e-9,
'Ar',
periodic=False)
distances.append(dist)
pitentials.append(pot)
sr.update(sys.r_array)
except StopIteration:
pass
#import pylab as pl
#pl.plot(distances, pitentials, 'o')
#pl.show()
v.schedule(update_pos)
v.run()
def test_forces():
'''This test simply shows two atoms that are subject to a lennard
jones potential. you can modulate the distance between atoms and
see if this physically makes sense. For example two atoms at a
distance of about 1.5sigma should bounce.
'''
import pyglet
pyglet.options['vsync'] = False
# Let's say we have to store this in nm and picoseconds
# I setup argon atoms pretty overlapping
a = Atom("Ar", [0.0, 0.0, 0.0])
b = Atom("Ar", [1.00, 0.0, 0.0])
sys = MonatomicSystem([a, b], 3.0)
v = Viewer()
sr = v.add_renderer(SphereRenderer, sys.atoms)
v.add_renderer(CubeRenderer, sys.boxsize)
# evo takes times in picoseconds
evo = evolve_generator(sys, t=1e2, tstep=0.002, periodic=False)
distances = [np.linalg.norm(sys.r_array[0] - sys.r_array[1])]
pitentials = [
cenergy.lennard_jones(sys.r_array * 1e-9, 'Ar', periodic=False)
]
def update_pos():
try:
for i in range(100):
sys, t = evo.next()
dist = np.linalg.norm(sys.r_array[0] - sys.r_array[1])
pot = cenergy.lennard_jones(sys.r_array * 1e-9,
'Ar',
periodic=False)
distances.append(dist)
pitentials.append(pot)
sr.update(sys.r_array)
except StopIteration:
import pylab as pl
pl.plot(distances, pitentials, 'o')
pl.show()
v.schedule(update_pos)
v.run()
def test_1():
boxsize = 50.0
sys = MonatomicSystem.random("Ne",500, boxsize)
#x, y = pair_correlation(sys, 20)
#pl.plot(x, y)
for i in range(1000):
print "Step ", i
farray = forces.lennard_jones(sys.r_array, "Ne", periodic=boxsize)
# Just this time let's assume masses are 1
sys.r_array, sys.varray = integrators.euler(sys.r_array, sys.varray, farray/300.17, 0.011)
# Add more periodic conditions
rarray = sys.r_array
i_toopositive = rarray > boxsize * 0.5
rarray[i_toopositive] -= boxsize
i_toonegative = rarray < - boxsize * 0.5
rarray[i_toonegative] += boxsize
sys.r_array = rarray
def test_2():
boxsize = 15.0 #nm
nmol = 400
sys = MonatomicSystem.random("Ar", nmol, boxsize)
v = Viewer()
pr = v.add_renderer(SphereRenderer, sys.atoms)
v.add_renderer(CubeRenderer, boxsize)
sys.varray = (np.random.rand(nmol, 3).astype(np.float32) - 0.5)
gen = evolve_generator(sys, t=1000, tstep=0.002, periodic=True)
def iterate(dt):
for i in range(10):
sys, t = gen.next()
pr.update(sys.r_array)
import pyglet
pyglet.clock.schedule(iterate)
pyglet.app.run()
