def test_replace_in_fort3_sort_new_replace_args_non_bonds():
tol = 1e-14
atom_names, _, _, _, _, non_bonds, _, _, _ = _parse_fort_3_file(file_name)
repl = (
Fort3Replacement('non bond', replace=True, content=['O', 'O', 4, 2]),
Fort3Replacement('non bond', replace=True, content=['H', 'H', 7, 6]),
Fort3Replacement('non bond', new=True, content=['Be', 'H', 9.1, 3.6]),
Fort3Replacement('non bond', new=True, content=['H+', 'O', 9.4, 3.3]),
)
non_bonds_new = _sort_new_replace_args_bonds(atom_names,
non_bonds,
*repl,
non_bond=True)
assert len(non_bonds_new) == 4
names = [('O', 'O'), ('H', 'H'), ('Be', 'H'), ('H+', 'O')]
lengths = [4.0, 7.0, 9.1, 9.4]
epsilons = [2.0, 6.0, 3.6, 3.3]
for name, length, eps in zip(names, lengths, epsilons):
found = False
n1, n2 = name
for non_bond in non_bonds_new:
name_1, name_2 = non_bond._content[:2]
if (((name_1 == n1) and (name_2 == n2))
or ((name_1 == n2) and (name_2 == n1))):
found = True
assert non_bond._content[2] == pytest.approx(length, abs=tol)
assert non_bond._content[3] == pytest.approx(eps, abs=tol)
assert found
def test_replace_in_fort3_sort_new_replace_args_atoms():
tol = 1e-14
atom_names, atoms, _, _, _, _, _, _, _ = _parse_fort_3_file(file_name)
repl = (
Fort3Replacement('atom', new=True, content=['P', 30.973, 0.0]),
Fort3Replacement('atom', replace=True, content=['O', 16.000, 0.0]),
Fort3Replacement('atom', new=True, content=['Ar-', 39.948, -1.0]),
)
atom_names, atoms = _sort_new_replace_args_atom(atom_names, atoms, *repl)
assert len(atoms) == 6
assert atoms[0]._content[0] == 'O'
assert atoms[0]._content[1] == pytest.approx(16.0, abs=tol)
for name, mass, charge in zip(['P', 'Ar-'], [30.973, 39.948], [0.0, -1.0]):
found = False
assert name in atom_names.values()
for atom in atoms[4:]:
if name == atom._content[0]:
found = True
assert atom._content[1] == pytest.approx(mass, abs=tol)
assert atom._content[2] == pytest.approx(charge, abs=tol)
assert found
caught = False
repl = (
Fort3Replacement('atom', new=True, content=['Ar', 0]),
Fort3Replacement('atom', new=True, content=['O', 1, 0]),
Fort3Replacement('atom', replace=True, content=['not', 1, 0]),
)
for r in repl:
try:
_sort_new_replace_args_atom(atom_names, atoms, r)
except ValueError:
caught = True
assert caught is True
def test_replace_in_fort3_sort_new_replace_args_angles():
tol = 1e-14
atom_names, _, _, angles, _, _, _, _, _ = _parse_fort_3_file(file_name)
repl = (
Fort3Replacement('angle', replace=True, content=['O', 'O', 'O', 4, 2]),
Fort3Replacement('angle', replace=True, content=['O', 'H', 'O', 7, 6]),
Fort3Replacement('angle', replace=True, content=['H', 'O', 'O', 3, 1]),
Fort3Replacement('angle', new=True, content=['Be', 'H', 'H', 9, 3]),
Fort3Replacement('angle', new=True, content=['H', 'O', 'H', 9.4, 3.3]),
)
angles_new = _sort_new_replace_args_angles(atom_names, angles, *repl)
assert len(angles_new) == 7
names = [('O', 'O', 'O'), ('O', 'H', 'O'), ('Be', 'H', 'H'),
('H', 'O', 'H'), ('O', 'O', 'H')]
lengths = [4.0, 7.0, 9.0, 9.4, 3.0]
epsilons = [2.0, 6.0, 3.0, 3.3, 1.0]
for name, length, eps in zip(names, lengths, epsilons):
found = False
n1, n2, n3 = name
for angle in angles_new:
name_1, name_2, name_3 = angle._content[:3]
if name_2 == n2:
if (name_1 == n1) and (name_3 == n3):
found = True
assert angle._content[3] == pytest.approx(length, abs=tol)
assert angle._content[4] == pytest.approx(eps, abs=tol)
break
elif (name_3 == n1) and (name_1 == n3):
found = True
assert angle._content[3] == pytest.approx(length, abs=tol)
assert angle._content[4] == pytest.approx(eps, abs=tol)
break
assert found
for n1, n2, n3 in zip(['not', 'H', 'O'], ['H', 'not', 'O'],
['H', 'O', 'not']):
caught = False
repl = Fort3Replacement('angle', new=True, content=[n1, n2, n3, 0, 0]),
try:
_sort_new_replace_args_angles(atom_names, angles, *repl)
except ValueError:
caught = True
assert caught is True
repl = (
Fort3Replacement('angle', new=True, content=['O', 'H', 0, 0]),
Fort3Replacement('angle', new=True, content=['O', 'O', 'O', 0, 0]),
Fort3Replacement('angle', replace=True, content=['.', 'H', 'A', 0, 0]),
Fort3Replacement('angle', new=True, content=['not', 'O', 0, 0]),
Fort3Replacement('angle', replace=True, content=['O', 'O', 'H+', 0,
0]),
)
for r in repl:
caught = False
try:
_sort_new_replace_args_angles(atom_names, angles, r)
except ValueError:
caught = True
assert caught is True
def test_replace_in_fort3_write_fort3_from_replace_objects():
atom_names, atoms, bonds, angles, torsions, non_bonds, scf, kappa, chi = (
_parse_fort_3_file(file_name))
out_path = os.path.join(os.path.dirname(os.path.abspath(file_name)),
'example_fort.3_out')
_write_fort3_from_replace_objects(atom_names, atoms, bonds, angles,
torsions, non_bonds, scf, kappa, chi,
atom_names, out_path)
os.remove(out_path)
def test_replace_in_fort3():
repl = (
Fort3Replacement(property='atom', new=True, content=['Ar', 1.67, 0]),
Fort3Replacement(property='atom', replace=True, content=['O', 16, 0]),
Fort3Replacement(property='bond type',
new=True,
content=['Be', 'Be', 7.41, 5.42]),
Fort3Replacement(property='bond type',
replace=True,
content=['H', 'O', 3.1, 9]),
Fort3Replacement(property='angle',
new=True,
content=['H', 'H', 'H', 84.1, 5.9]),
Fort3Replacement(property='angle',
replace=True,
content=['O', 'H', 'O', 16, 1]),
)
out_file = replace_in_fort3(file_name, None, *repl)
with open(out_file, 'r') as in_file:
lines = in_file.readlines()
atom_name, _, _, _, _, _, _, _, _ = _parse_fort_3_file(out_file)
ind = {val: key for key, val in atom_name.items()}
expected = [
f"{ind['Ar']} Ar 1.67 0.0", f"{ind['O']} O 16.0 0.0",
f"{ind['Be']} {ind['Be']} 7.41 5.42", f"{ind['H']} {ind['O']} 3.1 9.0",
f"{ind['H']} {ind['H']} {ind['H']} 84.1 5.9",
f"{ind['O']} {ind['H']} {ind['O']} 16.0 1.0"
]
for e in expected:
found = False
se = e.split()
for line in lines:
sline = line.split()
if len(se) == len(sline):
equal = True
for a, b in zip(se, sline):
equal = _check_equal(a, b) and equal
if equal is True:
found = True
break
assert found is True
caught = False
repl = Fort3Replacement(property='bond type', content=['H', 'H', 1, 1])
try:
out_file = replace_in_fort3(file_name, None, repl)
except ValueError:
caught = True
assert caught is True
if os.path.exists(out_file) and os.path.isfile(out_file):
os.remove(out_file)
def test_replace_in_fort3_replace_scf():
inps = [[3, 4, 5], (3, 4, 5), '3 4 5', ['3 4 5'], np.array([3, 4, 5])]
for scf_new in inps:
replace_1 = Fort3Replacement(property='scf',
replace=True,
content=scf_new)
out_path = replace_in_fort3(file_name, None, replace_1)
_, _, _, _, _, _, scf, _, _ = _parse_fort_3_file(out_path)
for expected, found in zip([3, 4, 5], scf):
assert expected == found
inps = [9, np.array([9]), [9], (9), '9']
for scf_new in inps:
replace_1 = Fort3Replacement(property='scf',
replace=True,
content=scf_new)
out_path = replace_in_fort3(file_name, None, replace_1)
_, _, _, _, _, _, scf, _, _ = _parse_fort_3_file(out_path)
for expected, found in zip([9, 9, 9], scf):
assert expected == found
os.remove(out_path)
def test_replace_in_fort3_sort_new_replace_args_bonds():
tol = 1e-14
atom_names, _, bonds, _, _, _, _, _, _ = _parse_fort_3_file(file_name)
repl = (
Fort3Replacement('bond type', replace=True, content=['H', 'O', 4, 2]),
Fort3Replacement('bond type', replace=True, content=['H+', 'H', 7, 6]),
Fort3Replacement('bond type', new=True, content=['H', 'H', 9.1, 3.6]),
Fort3Replacement('bond type', new=True, content=['H+', 'O', 9.4, 3.3]),
)
bonds_new = _sort_new_replace_args_bonds(atom_names, bonds, *repl)
assert len(bonds_new) == 5
names = [('H', 'O'), ('H+', 'H'), ('H', 'H'), ('H+', 'O')]
lengths = [4.0, 7.0, 9.1, 9.4]
epsilons = [2.0, 6.0, 3.6, 3.3]
for name, length, eps in zip(names, lengths, epsilons):
found = False
n1, n2 = name
for bond in bonds_new:
name_1, name_2 = bond._content[:2]
if (((name_1 == n1) and (name_2 == n2))
or ((name_1 == n2) and (name_2 == n1))):
found = True
assert bond._content[2] == pytest.approx(length, abs=tol)
assert bond._content[3] == pytest.approx(eps, abs=tol)
assert found
for n1, n2 in zip(['not', 'H'], ['H', 'not']):
caught = False
repl = Fort3Replacement('bond type', new=True, content=[n1, n2, 0, 0]),
try:
_sort_new_replace_args_bonds(atom_names, bonds, *repl)
except ValueError:
caught = True
assert caught is True
repl = (
Fort3Replacement('bond type', new=True, content=['O', 0, 0]),
Fort3Replacement('bond type', new=True, content=['O', 'O', 0, 0]),
Fort3Replacement('bond type', replace=True, content=['.', 'H', 0, 0]),
Fort3Replacement('bond type', new=True, content=['H', 'O', 0, 0]),
Fort3Replacement('bond type', replace=True, content=['H', 'H', 0, 0]),
)
for r in repl:
caught = False
try:
_sort_new_replace_args_bonds(atom_names, bonds, r)
except ValueError:
caught = True
assert caught is True
def test_replace_in_fort3_parse_fort_3_file():
tol = 1e-14
atom_names, atoms, bonds, angles, torsions, non_bonds, scf, kappa, chi = (
_parse_fort_3_file(file_name))
expected_names = ['O', 'H', 'Be', 'H+']
for name in expected_names:
assert name in atom_names.values()
expected_masses = [15.999, 1.008, 9.012, 1.007]
expected_charges = [0.0, 0.0, 0.0, 1.0]
for name, mass, charge, atom in zip(expected_names, expected_masses,
expected_charges, atoms):
assert name == atom._content[0]
assert mass == pytest.approx(atom._content[1], abs=tol)
assert charge == pytest.approx(atom._content[2], abs=tol)
expected_bonds = [(1, 1), (1, 2), (2, 4)]
expected_bond_lengths = [3.21, 2.01, 5.98]
expected_bond_eps = [2.4, 1.7, 8.8]
for ind, length, eps, bond in zip(expected_bonds, expected_bond_lengths,
expected_bond_eps, bonds):
for a, b in zip(ind, bond._content[:2]):
assert atom_names[a] == b
assert bond._content[2] == pytest.approx(length, abs=tol)
assert bond._content[3] == pytest.approx(eps, abs=tol)
expected_bond_angles = [(1, 1, 1), (1, 2, 1), (3, 4, 3), (4, 4, 4)]
expected_bond_theta = [75.0, 64.1, 90.9, 71.0]
expected_bond_eps = [7.1, 4.0, 1.6, 17.2]
for ind, theta, eps, angle in zip(expected_bond_angles,
expected_bond_theta, expected_bond_eps,
angles):
for a, b in zip(ind, angle._content[:3]):
assert atom_names[a] == b
assert angle._content[3] == pytest.approx(theta, abs=tol)
assert angle._content[4] == pytest.approx(eps, abs=tol)
expected_torsions = [(1, 2, 3, 4), (2, 2, 2, 2)]
expected_torsion_phi = [75.0, 12.5]
expected_torsion_eps = [27.78, 0.24]
for ind, theta, eps, torsion in zip(expected_torsions,
expected_torsion_phi,
expected_torsion_eps, torsions):
for a, b in zip(ind, torsion._content[:4]):
assert atom_names[a] == b
assert torsion._content[4] == pytest.approx(theta, abs=tol)
assert torsion._content[5] == pytest.approx(eps, abs=tol)
expected_non_bonds = [(1, 1), (2, 2)]
expected_non_bond_sigma = [1.8, 3.2]
expected_non_bond_eps = [29.14, 2.349]
for ind, sigma, eps, bond in zip(expected_non_bonds,
expected_non_bond_sigma,
expected_non_bond_eps, non_bonds):
for a, b in zip(ind, bond._content[:2]):
assert atom_names[a] == b
assert bond._content[2] == pytest.approx(sigma, abs=tol)
assert bond._content[3] == pytest.approx(eps, abs=tol)
for m, expected in zip(scf, [5, 5, 10]):
assert m == expected
assert kappa == pytest.approx(1.204, abs=tol)
expected_chi = [[0, 1, 0, -4], [1, 0, 2, 0], [0, 2, 0, 3], [-4, 0, 3, 0]]
assert np.allclose(expected_chi, chi)