def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]), ])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.type_array, ['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([
Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(
s.type_array,
['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
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)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6)))
#assert_npequal(s.bond_orders)
# 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]]))
# This doesn't change the bond_ordering
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
import inspect
ss2 = System.from_arrays(**dict(inspect.getmembers(ss)))
ss2.r_array += 10.0
ms = merge_systems(ss, ss2)
assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]]))
assert_npequal(ms.bond_orders, np.array([1, 1]))
# From_arrays
s = System.from_arrays(mol_indices=[0], bonds=bz.bonds, **bz.__dict__)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(s.bond_orders, bz.bond_orders)
# Get molecule entry
# Test the bonds when they're 0
s.bonds = np.array([])
assert_equals(s.get_derived_molecule_array('formula'), 'C6')
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)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6)))
#assert_npequal(s.bond_orders)
# 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]]))
# This doesn't change the bond_ordering
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
import inspect
ss2 = System.from_arrays(**dict(inspect.getmembers(ss)))
ss2.r_array += 10.0
ms = merge_systems(ss, ss2)
assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]]))
assert_npequal(ms.bond_orders, np.array([1, 1]))
# From_arrays
s = System.from_arrays(mol_indices=[0], bonds=bz.bonds, **bz.__dict__)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(s.bond_orders, bz.bond_orders)
# Get molecule entry
# Test the bonds when they're 0
s.bonds = np.array([])
assert_equals(s.get_derived_molecule_array('formula'), 'C6')
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_subsystem_from_molecules(self):
mols = self._make_molecules()
system = System(mols)
subsystem = subsystem_from_molecules(system, np.array([0, 2]))
assert_equals(subsystem.n_mol, 2)
def test_subsystem_from_molecules(self):
mols = self._make_molecules()
system = System(mols)
subsystem = subsystem_from_molecules(system, np.array([0, 2]))
assert_equals(subsystem.n_mol, 2)
