def test_bonds(self):
frame = Frame()
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_bond(0, 1)
frame.add_bond(3, 4)
frame.add_bond(2, 1, BondOrder.Qintuplet)
self.assertEqual(frame.topology.bonds.all(),
np.array([[0, 1], [1, 2], [3, 4]]).all())
self.assertEqual(
frame.topology.bonds_orders,
[BondOrder.Unknown, BondOrder.Qintuplet, BondOrder.Unknown])
frame.remove_bond(3, 4)
# Also try to remove non-existing bonds
frame.remove_bond(3, 4)
frame.remove_bond(0, 4)
self.assertEqual(frame.topology.bonds.all(),
np.array([[0, 1], [1, 2]]).all())
def test_distance(self):
frame = Frame()
frame.cell = UnitCell(3.0, 4.0, 5.0)
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (1, 2, 6))
self.assertEqual(frame.distance(0, 1), math.sqrt(6.0))
def test_name(self):
atom = Atom("He")
self.assertEqual(atom.name, "He")
self.assertEqual(atom.full_name, "Helium")
atom.name = "Zn"
self.assertEqual(atom.name, "Zn")
def test_angle(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
self.assertEqual(frame.angle(0, 1, 2), math.pi / 2.0)
def test_property(self):
atom = Atom("He")
atom["foo"] = 3
self.assertEqual(atom["foo"], 3.0)
atom["foo"] = False
self.assertEqual(atom["foo"], False)
with remove_warnings:
with self.assertRaises(ChemfilesError):
_ = atom["bar"]
with self.assertRaises(ChemfilesError):
atom[3] = "test"
with self.assertRaises(ChemfilesError):
_ = atom[3]
# Check that enabling indexing/__getitem__ did not enable iteration
with self.assertRaises(TypeError):
for i in atom:
pass
atom["bar"] = "baz"
self.assertEqual(atom.properties_count(), 2)
self.assertEqual(set(atom.list_properties()), {"bar", "foo"})
def test_out_of_plane(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (0, 0, 3))
self.assertEqual(frame.out_of_plane(1, 3, 0, 2), 3.0)
def test_dihedral(self):
frame = Frame()
frame.add_atom(Atom(""), (1, 0, 0))
frame.add_atom(Atom(""), (0, 0, 0))
frame.add_atom(Atom(""), (0, 1, 0))
frame.add_atom(Atom(""), (-1, 1, 0))
self.assertEqual(frame.dihedral(0, 1, 2, 3), math.pi)
def test_copy(self):
atom = Atom("He")
cloned = copy.copy(atom)
self.assertEqual(atom.name, "He")
self.assertEqual(cloned.name, "He")
atom.name = "Zn"
self.assertEqual(atom.name, "Zn")
self.assertEqual(cloned.name, "He")
def test_add_atom(self):
frame = Frame()
frame.add_atom(Atom("F"), (3, 4, 5))
self.assertEqual(len(frame.atoms), 1)
self.assertEqual(list(frame.positions[0]), [3, 4, 5])
frame.add_velocities()
frame.add_atom(Atom("F"), (-3, -4, 5), (1, 0, 1))
self.assertEqual(list(frame.positions[1]), [-3, -4, 5])
self.assertEqual(list(frame.velocities[1]), [1, 0, 1])
def test_topology(self):
frame = Frame()
frame.resize(2)
topology = Topology()
topology.atoms.append(Atom("Zn"))
topology.atoms.append(Atom("Ar"))
frame.topology = topology
self.assertEqual(frame.atoms[0].name, "Zn")
self.assertEqual(frame.atoms[1].name, "Ar")
def test_type(self):
atom = Atom("He")
self.assertEqual(atom.type, "He")
self.assertEqual(atom.full_name, "Helium")
atom.type = "Zn"
self.assertEqual(atom.type, "Zn")
self.assertEqual(atom.full_name, "Zinc")
atom = Atom("He2", "H")
self.assertEqual(atom.name, "He2")
self.assertEqual(atom.type, "H")
def testing_frame():
frame = Frame()
frame.add_atom(Atom("H"), [0, 0, 0])
frame.add_atom(Atom("O"), [0, 0, 0])
frame.add_atom(Atom("O"), [0, 0, 0])
frame.add_atom(Atom("H"), [0, 0, 0])
frame.add_bond(0, 1)
frame.add_bond(1, 2)
frame.add_bond(2, 3)
return frame
def test_size(self):
topology = Topology()
self.assertEqual(len(topology.atoms), 0)
topology.atoms.append(Atom("H"))
topology.atoms.append(Atom("O"))
topology.atoms.append(Atom("O"))
topology.atoms.append(Atom("H"))
self.assertEqual(len(topology.atoms), 4)
topology.resize(8)
self.assertEqual(len(topology.atoms), 8)
topology.atoms.remove(3)
self.assertEqual(len(topology.atoms), 7)
del topology.atoms[4]
self.assertEqual(len(topology.atoms), 6)
def test_indexes(self):
# Create an input file
frame = Frame()
for i in range(120):
frame.add_atom(Atom('X'), [i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("filename.xyz", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "indexes.py")
# disable output
exec(open(path).read(), globals(), {'print': lambda _: None})
def test_select(self):
# Create an input file
frame = Frame()
NAMES = ["N", "Zn", "C", "O"]
for i in range(120):
frame.add_atom(Atom(NAMES[i % 4]),
[i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("input.arc", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "select.py")
exec(open(path).read(), globals())
def test_read(self):
trajectory = Trajectory(get_data_path("water.xyz"))
self.assertEqual(trajectory.nsteps, 100)
self.assertEqual(trajectory.path, get_data_path("water.xyz"))
frame = trajectory.read()
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.positions[0].all(),
np.array([0.417219, 8.303366, 11.737172]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.099554, -0.045104, 14.153846]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.atoms[0].name, "O")
self.assertEqual(frame.atoms[1].name, "H")
trajectory.set_cell(UnitCell(30, 30, 30))
frame = trajectory.read_step(41)
self.assertEqual(frame.cell.lengths, (30.0, 30.0, 30.0))
self.assertEqual(frame.positions[0].all(),
np.array([0.761277, 8.106125, 10.622949]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.13242, 0.079862, 14.194161]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.topology.bonds_count(), 0)
frame.guess_bonds()
self.assertEqual(frame.topology.bonds_count(), 181)
self.assertEqual(frame.topology.angles_count(), 87)
topology = Topology()
for i in range(297):
topology.atoms.append(Atom("Cs"))
trajectory.set_topology(topology)
frame = trajectory.read_step(10)
self.assertEqual(frame.atoms[10].name, "Cs")
trajectory.set_topology(get_data_path("topology.xyz"), "XYZ")
frame = trajectory.read()
self.assertEqual(frame.atoms[100].name, "Rd")
def test_write(self):
frame = Frame()
for i in range(4):
frame.add_atom(Atom("X"), [1, 2, 3])
with Trajectory("test-tmp.xyz", "w") as fd:
fd.write(frame)
expected_content = """4
Written by the chemfiles library
X 1 2 3
X 1 2 3
X 1 2 3
X 1 2 3
"""
with open("test-tmp.xyz") as fd:
self.assertEqual(fd.read(), expected_content)
os.unlink("test-tmp.xyz")
def test_mass(self):
atom = Atom("He")
self.assertAlmostEqual(atom.mass, 4.002602, 6)
atom.mass = 1.0
self.assertEqual(atom.mass, 1.0)
def test_very_long_name(self):
atom = Atom("He" * 128)
self.assertEqual(atom.name, "He" * 128)
def test_repr(self):
self.assertEqual(Atom("He").__repr__(), "Atom('He')")
self.assertEqual(Atom("He-3", "He").__repr__(), "Atom('He-3', 'He')")
def test_charge(self):
atom = Atom("He")
self.assertEqual(atom.charge, 0.0)
atom.charge = -1.5
self.assertEqual(atom.charge, -1.5)
if state < 7:
x1, y1, x2, y2, x3, y3, z3 = coordinate_si(
ring, column, state)
if state > 6 and ring % 4 == 1 and column % 2 == 0: #up (vert)
x1, y1, x2, y2, x3, y3, z3 = coordinate_up(
ring, column, state)
if state > 6 and ring % 4 == 1 and column % 2 == 1: #down (rouge)
x1, y1, x2, y2, x3, y3, z3 = coordinate_down(
ring, column, state)
if state > 6 and ring % 4 == 3 and column % 2 == 1: #up (vert)
x1, y1, x2, y2, x3, y3, z3 = coordinate_up(
ring, column, state)
if state > 6 and ring % 4 == 3 and column % 2 == 0: #down (rouge)
x1, y1, x2, y2, x3, y3, z3 = coordinate_down(
ring, column, state)
if state < 7 and state > 0:
atom1 = Atom("Si", "Si")
atom2 = Atom("O", "O")
atom3 = Atom("H", "H")
frame.add_atom(atom1, [x1, y1, 0])
frame.add_atom(atom2, [x2, y2, height])
frame.add_atom(atom3, [x3, y3, height])
if state > 7:
atom1 = Atom("Ow", "O")
atom2 = Atom("Hw", "H")
atom3 = Atom("Hw", "H")
frame.add_atom(atom1, [x1, y1, height])
frame.add_atom(atom2, [x2, y2, height])
frame.add_atom(atom3, [x3, y3, z3])
ring += 1
# This file is an example for the chemfiles library
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
import numpy as np
from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
topology = Topology()
topology.atoms.append(Atom("H"))
topology.atoms.append(Atom("O"))
topology.atoms.append(Atom("H"))
topology.add_bond(0, 1)
topology.add_bond(2, 1)
frame = Frame()
frame.resize(3)
frame.topology = topology
frame.positions[0, :] = np.array([1.0, 0.0, 0.0])
frame.positions[1, :] = np.array([0.0, 0.0, 0.0])
frame.positions[2, :] = np.array([0.0, 1.0, 0.0])
frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
frame.add_bond(3, 4)
frame.add_bond(4, 5)
frame.cell = UnitCell(10, 10, 10)
def test_radii(self):
self.assertAlmostEqual(Atom("He").vdw_radius, 1.4, 2)
self.assertAlmostEqual(Atom("He").covalent_radius, 0.32, 3)
self.assertEqual(Atom("H1").vdw_radius, 0)
self.assertEqual(Atom("H1").covalent_radius, 0)
def test_atomic_number(self):
self.assertEqual(Atom("He").atomic_number, 2)
self.assertEqual(Atom("H1").atomic_number, 0)
