def test_linear_displacement(deg):
from pysisyphus.intcoords.LinearDisplacement import LinearDisplacement
from pysisyphus.helpers import geom_loader
zmat_str = f"""
C
C 1 1.5
C 1 1.5 2 {deg}
"""
zmat = zmat_from_str(zmat_str)
geom = geom_from_zmat(zmat)
coords3d = geom.coords3d
indices = [1, 0, 2]
ld = LinearDisplacement(indices)
val, grad = ld.calculate(coords3d, gradient=True)
# First derivative
ref_row = np.zeros_like(coords3d)
ref_row[indices] = fin_diff_prim(ld, coords3d).reshape(-1, 3)
ref_row = ref_row.flatten()
np.testing.assert_allclose(grad, ref_row, atol=1e-10)
# Second derivative
# Code generated 2nd derivative
dgrad = ld.jacobian(coords3d)
mp_dgrad = mp_d.d2q_ld(*coords3d[indices].flatten(), *ld.cross_vec)
# Finite difference reference values
ref_dgrad = fin_diff_B(ld, coords3d)
np.testing.assert_allclose(dgrad, ref_dgrad, atol=1e-9)
np.testing.assert_allclose(mp_dgrad, ref_dgrad, atol=1e-9)
def test_linear_bend(deg):
indices = [1, 0, 2]
zmat_str = f"""
C
C 1 1.5
C 1 1.5 2 {deg}
""".strip()
zmat = zmat_from_str(zmat_str)
geom = geom_from_zmat(zmat)
coords3d = geom.coords3d
# Explicitly implemented
# Gradient returned in order [0, 1, 2]
val, grad = LinearBend._calculate(coords3d, indices, gradient=True)
# Orthogonal direction
w = LinearBend._get_orthogonal_direction(coords3d, indices)
# Reference values, code generated
args = coords3d[indices].flatten()
ref_val = q_lb(*args, *w)
# Reference gradient returned in order [1, 0, 2]
_ref_grad = dq_lb(*args, *w)
ref_grad = np.zeros_like(coords3d)
ref_grad[indices] = _ref_grad.reshape(-1, 3)
assert val == pytest.approx(ref_val)
np.testing.assert_allclose(grad.flatten(), ref_grad.flatten(), atol=1e-12)
def assert_geom(ref_fn, zmat_fn, atol=2.5e-5):
zmat = zmat_from_fn(zmat_fn)
geom = geom_from_zmat(zmat)
ref = geom_loader(ref_fn)
rmsd = kabsch_rmsd(geom.coords3d, ref.coords3d, translate=True)
print(f"RMSD: {rmsd:.6f}")
assert rmsd == pytest.approx(0., abs=atol)
def test_torsion(dihedral):
indices = [3, 2, 0, 1]
zmat_str = f"""
C
C 1 1.
C 1 1. 2 135.
C 3 1. 1 135. 2 {dihedral}
""".strip()
zmat = zmat_from_str(zmat_str)
geom = geom_from_zmat(zmat)
coords3d = geom.coords3d
# Explicitly implemented
# Gradient returned in order [3, 2, 0, 1]
val, grad = Torsion._calculate(coords3d, indices, gradient=True)
sign = np.sign(val)
# Reference values, code generated
args = coords3d[indices].flatten()
ref_val = q_d(*args)
# Reference gradient returned in order [3, 2, 0, 1]
_ref_grad = dq_d(*args)
ref_grad = np.zeros_like(coords3d)
ref_grad[indices] = _ref_grad.reshape(-1, 3)
mp_ref_val = mp_d.q_d(*args)
_mp_ref_grad = mp_d.dq_d(*args)
mp_ref_grad = np.zeros_like(coords3d)
mp_ref_grad[indices] = _mp_ref_grad.reshape(-1, 3)
# Sign change is not taken into account in q_d
assert val == pytest.approx(sign * ref_val, abs=1e-8), "Dihedral value"
assert val == pytest.approx(sign * mp_ref_val, abs=1e-8)
np.testing.assert_allclose(grad.flatten(),
sign * ref_grad.flatten(),
atol=1e-8,
err_msg="1st derivative")
np.testing.assert_allclose(
grad.flatten(),
sign * mp_ref_grad.flatten(),
atol=1e-8,
err_msg="1st derivative",
)
# Code generated 2nd derivative
dgrad = sign * d2q_d(*args)
mp_dgrad = sign * mp_d.d2q_d(*args)
# Finite difference reference values
ref_dgrad = fin_diff_B(Torsion(indices), coords3d)
np.testing.assert_allclose(dgrad,
ref_dgrad,
atol=1e-8,
err_msg="2nd derivative")
np.testing.assert_allclose(mp_dgrad,
ref_dgrad,
atol=1e-8,
err_msg="2nd derivative")
def test_geom_from_zmat(this_dir):
zmat = [
ZLine("C"),
ZLine("C", 0, 1.510486 * AB),
ZLine("N", 0, 1.459785 * AB, 1, 112.257683),
ZLine("O", 1, 1.220389 * AB, 0, 118.653885, 2, -179.541229),
ZLine("O", 1, 1.353023 * AB, 0, 122.591621, 2, 0.825231),
]
geom = geom_from_zmat(zmat)
reference = geom_loader(this_dir / "glycine_noh.xyz")
rmsd = kabsch_rmsd(geom.coords3d, reference.coords3d, translate=True)
assert rmsd == pytest.approx(0., abs=1e-6)
def test_bend(deg):
indices = [1, 0, 2]
zmat_str = f"""
C
C 1 1.5
C 1 1.5 2 {deg}
""".strip()
zmat = zmat_from_str(zmat_str)
geom = geom_from_zmat(zmat)
coords3d = geom.coords3d
# Explicitly implemented
# Gradient returned in order [0, 1, 2]
val, grad = Bend._calculate(coords3d, indices, gradient=True)
# Reference values, code generated
args = coords3d[indices].flatten()
ref_val = q_a(*args)
# Reference gradient returned in order [1, 0, 2]
_ref_grad = dq_a(*args)
ref_grad = np.zeros_like(coords3d)
ref_grad[indices] = _ref_grad.reshape(-1, 3)
mp_ref_val = mp_d.q_a(*args)
_mp_ref_grad = mp_d.dq_a(*args)
mp_ref_grad = np.zeros_like(coords3d)
mp_ref_grad[indices] = _mp_ref_grad.reshape(-1, 3)
assert val == pytest.approx(ref_val)
assert val == pytest.approx(mp_ref_val)
np.testing.assert_allclose(grad.flatten(), ref_grad.flatten(), atol=1e-12)
np.testing.assert_allclose(grad.flatten(),
mp_ref_grad.flatten(),
atol=1e-12)
# Code generated 2nd derivative
dgrad = d2q_a(*args)
mp_dgrad = mp_d.d2q_a(*args)
# Finite difference reference values
ref_dgrad = fin_diff_B(Bend(indices), coords3d)
np.testing.assert_allclose(dgrad, ref_dgrad, atol=1e-9)
np.testing.assert_allclose(mp_dgrad, ref_dgrad, atol=1e-9)
