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_1():
a = Atom("Ne", [-1.0, 0.0, 0.0])
b = Atom("Ne", [1.0, 0.0, 0.0])
am = Molecule([a, b])
# Force vector exterted on the first atom TODO, for optimization
# purposes, this function should not take atom objects but coords.
f = lennard_jones(a, b)
def _make_water():
mol = Molecule([
Atom("O", [-4.99, 2.49, 0.0]),
Atom("H", [-4.02, 2.49, 0.0]),
Atom("H", [-5.32, 1.98, 1.0])
],
bonds=[[0, 1], [0, 2]],
export={'hello': 1.0})
return mol
def test_random():
'''Testing random made box'''
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = cdb.get("molecule", 'gromacs.spce')
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
def test_crystal():
'''Building a crystal by using spacegroup module'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[13, 13, 13])
def test_sort():
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
tsys.sort()
assert np.all(tsys.type_array[:tsys.n_mol / 2] == 'Cl')
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_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
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_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0],[0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3,3,3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
def test_bonds():
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
# Adding bonds
s = System.empty(2, 2 * bz.n_atoms)
s.add(bz)
assert_npequal(s.bonds, bz.bonds)
s.add(bz)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6)))
# Reordering
orig = np.array([[0, 1], [6, 8]])
s.bonds = orig
s.reorder_molecules([1, 0])
assert_npequal(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
ss2 = System.from_arrays(**ss.__dict__)
ss2.r_array += 10.0
ms = merge_systems(ss, ss2)
assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]]))
# From_arrays
s = System.from_arrays(mol_indices=[0], **bz.__dict__)
assert_npequal(s.bonds, bz.bonds)
# Get molecule entry
# Test the bonds when they're 0
s.bonds = np.array([])
assert_equals(s.get_derived_molecule_array('formula'), 'C6')