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_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_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_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_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_system():
wat = 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])], export={'hello': 1.0})
wat.r_array *= 0.1
# Initialization from empty
s = System.empty(4, 4*3)
mols = []
for i in xrange(s.n_mol):
wat.r_array += 0.1
s.add(wat)
m = wat.copy()
mols.append(wat.copy())
# Printing just to test if there aren't any exception
print "Init from Empty"
print "*" * 72
_print_sysinfo(s)
print "Init Normal"
print "*" * 72
s = System(mols)
_print_sysinfo(s)
# 3 water molecules
r_array = np.random.random((9, 3))
type_array = ['O', 'H', 'H', 'O', 'H', 'H', 'O', 'H', 'H']
mol_indices = [0, 3, 6]
mol_n_atoms = [3, 3, 3]
s2 = System.from_arrays(r_array=r_array, type_array=type_array,
mol_indices=mol_indices, mol_n_atoms=mol_n_atoms)
print 'bonds', s2._mol_bonds
sub2 = subsystem_from_molecules(s2, np.array([0, 2]))
assert sub2.n_mol == 2
sub = subsystem_from_atoms(s2, np.array([True, True, False,
False, False, False,
False, False, False]))
assert sub.n_mol == 1
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')
