import os
import tempfile
import pytest
import readcon
RESOURCES = os.path.join(os.path.dirname(__file__), "..", "..", "resources", "test")
def _resource(fname):
return os.path.join(RESOURCES, fname)
class TestReadCon:
def test_read_con_file(self):
frames = readcon.read_con(_resource("tiny_cuh2.con"))
assert len(frames) == 1
frame = frames[0]
assert len(frame) == 4
assert frame.cell[0] == pytest.approx(15.3456, abs=1e-4)
assert frame.angles[0] == pytest.approx(90.0)
assert not frame.has_velocities
def test_read_con_atoms(self):
frames = readcon.read_con(_resource("tiny_cuh2.con"))
atoms = frames[0].atoms
assert atoms[0].symbol == "Cu"
assert atoms[0].x == pytest.approx(0.6394, abs=1e-3)
assert atoms[0].is_fixed is True assert atoms[0].fixed == [True, True, True]
assert atoms[0].atom_id == 0
assert not atoms[0].has_velocity
assert atoms[0].vx is None
def test_read_multi_frame(self):
frames = readcon.read_con(_resource("tiny_multi_cuh2.con"))
assert len(frames) == 2
assert len(frames[0]) == 4
assert len(frames[1]) == 4
class TestReadConvel:
def test_read_convel(self):
frames = readcon.read_con(_resource("tiny_cuh2.convel"))
assert len(frames) == 1
frame = frames[0]
assert frame.has_velocities
atom = frame.atoms[0]
assert atom.has_velocity
assert atom.vx == pytest.approx(0.001234, abs=1e-6)
assert atom.vy == pytest.approx(0.002345, abs=1e-6)
def test_read_multi_convel(self):
frames = readcon.read_con(_resource("tiny_multi_cuh2.convel"))
assert len(frames) == 2
assert frames[0].has_velocities
assert frames[1].has_velocities
class TestReadForces:
def test_read_force_section(self):
frames = readcon.read_con(_resource("tiny_cuh2_forces.con"))
assert len(frames) == 1
frame = frames[0]
assert frame.has_forces
assert frame.energy == pytest.approx(-42.5)
assert frame.metadata["potential"]["type"] == "EMT"
atom = frame.atoms[0]
assert atom.has_forces
assert atom.fixed == [True, True, True]
assert atom.fx == pytest.approx(0.123456, abs=1e-6)
assert atom.fy == pytest.approx(0.234567, abs=1e-6)
assert atom.fz == pytest.approx(-0.345678, abs=1e-6)
class TestReadConString:
def test_read_string(self):
with open(_resource("tiny_cuh2.con")) as f:
contents = f.read()
frames = readcon.read_con_string(contents)
assert len(frames) == 1
assert len(frames[0]) == 4
class TestWriteCon:
def test_roundtrip(self):
frames = readcon.read_con(_resource("tiny_multi_cuh2.con"))
with tempfile.NamedTemporaryFile(suffix=".con", delete=False) as f:
tmppath = f.name
try:
readcon.write_con(tmppath, frames)
frames2 = readcon.read_con(tmppath)
assert len(frames2) == len(frames)
for orig, reread in zip(frames, frames2):
assert len(orig) == len(reread)
finally:
os.unlink(tmppath)
def test_write_string_roundtrip(self):
frames = readcon.read_con(_resource("tiny_cuh2.con"))
output = readcon.write_con_string(frames)
frames2 = readcon.read_con_string(output)
assert len(frames2) == len(frames)
assert len(frames2[0]) == len(frames[0])
class TestConvelWriteRoundtrip:
def test_convel_roundtrip(self):
frames = readcon.read_con(_resource("tiny_cuh2.convel"))
output = readcon.write_con_string(frames)
frames2 = readcon.read_con_string(output)
assert len(frames2) == 1
assert frames2[0].has_velocities
assert frames2[0].atoms[0].vx == pytest.approx(frames[0].atoms[0].vx, abs=1e-6)
class TestAtomConstructor:
def test_basic(self):
atom = readcon.Atom(symbol="Cu", x=1.0, y=2.0, z=3.0)
assert atom.symbol == "Cu"
assert atom.x == 1.0
assert atom.is_fixed is False
assert atom.fixed == [False, False, False]
assert atom.atom_id == 0
assert atom.mass is None
def test_with_mass(self):
atom = readcon.Atom(symbol="Cu", x=0.0, y=0.0, z=0.0, mass=63.546)
assert atom.mass == pytest.approx(63.546)
def test_with_velocity(self):
atom = readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0, vx=0.1, vy=0.2, vz=0.3)
assert atom.has_velocity
assert atom.vx == pytest.approx(0.1)
def test_repr(self):
atom = readcon.Atom(symbol="Cu", x=1.0, y=2.0, z=3.0, atom_id=5)
r = repr(atom)
assert "Cu" in r
assert "5" in r
class TestConFrameConstructor:
def test_build_frame(self):
atoms = [
readcon.Atom(symbol="Cu", x=0.0, y=0.0, z=0.0, fixed=[True, True, True], atom_id=0, mass=63.546),
readcon.Atom(symbol="Cu", x=1.0, y=1.0, z=1.0, fixed=[True, True, True], atom_id=1, mass=63.546),
readcon.Atom(symbol="H", x=2.0, y=2.0, z=2.0, fixed=[False, False, False], atom_id=2, mass=1.008),
]
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=atoms,
prebox_header=["header1", "header2"],
)
assert len(frame) == 3
assert frame.cell[0] == 10.0
assert frame.angles[2] == 90.0
assert not frame.has_velocities
def test_roundtrip(self):
atoms = [
readcon.Atom(symbol="Cu", x=0.123456789012345, y=0.0, z=0.0,
fixed=[True, True, True], atom_id=0, mass=63.546),
readcon.Atom(symbol="H", x=1.0, y=2.0, z=3.0,
fixed=[False, False, False], atom_id=1, mass=1.008),
]
frame = readcon.ConFrame(
cell=[15.0, 15.0, 100.0],
angles=[90.0, 90.0, 90.0],
atoms=atoms,
)
output = readcon.write_con_string([frame], precision=17)
frames2 = readcon.read_con_string(output)
assert len(frames2) == 1
assert frames2[0].atoms[0].x == pytest.approx(0.123456789012345, abs=1e-15)
def test_repr(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
r = repr(frame)
assert "natoms=1" in r
def test_typed_metadata_helpers(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
frame.set_energy(-1.25)
frame.set_frame_index(7)
frame.set_time(3.5)
frame.set_timestep(0.2)
frame.set_neb_bead(4)
frame.set_neb_band(2)
frame.set_scalar_metadata("convergence", 1.0e-3)
frame.set_string_metadata("generator", "eon")
assert frame.energy == pytest.approx(-1.25)
assert frame.frame_index == 7
assert frame.time == pytest.approx(3.5)
assert frame.timestep == pytest.approx(0.2)
assert frame.neb_bead == 4
assert frame.neb_band == 2
assert frame.metadata["convergence"] == pytest.approx(0.001)
assert frame.metadata["generator"] == "eon"
def test_set_metadata_json(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
frame.set_metadata_json(
'{"con_spec_version":2,"frame_index":5,"energy":-42.5,"generator":"test","sections":["forces"]}'
)
assert frame.frame_index == 5
assert frame.energy == pytest.approx(-42.5)
assert frame.metadata["generator"] == "test"
assert "sections" not in frame.metadata
def test_constructor_metadata(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
metadata={"generator": "pytest", "nested": {"ok": True}},
)
assert frame.metadata["generator"] == "pytest"
assert frame.metadata["nested"]["ok"] is True
def test_metadata_property_setter(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
frame.metadata = {"generator": "setter", "values": [1, 2.5, None]}
assert frame.metadata == {"generator": "setter", "values": [1, 2.5, None]}
def test_metadata_rejects_non_json_values(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
with pytest.raises(ValueError):
frame.metadata = {"bad": object()}
def test_metadata_item_assignment_persists_through_writes(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
frame.metadata["generator"] = "item-setter"
frame.metadata["nested"] = {"values": [1, 2.5, None], "ok": True}
output = readcon.write_con_string([frame])
reread = readcon.read_con_string(output)[0]
assert reread.metadata["generator"] == "item-setter"
assert reread.metadata["nested"]["values"] == [1, 2.5, None]
assert reread.metadata["nested"]["ok"] is True
with tempfile.NamedTemporaryFile(suffix=".con", delete=False) as f:
tmppath = f.name
try:
readcon.write_con(tmppath, [frame])
from_file = readcon.read_con(tmppath)[0]
assert from_file.metadata["generator"] == "item-setter"
assert from_file.metadata["nested"]["values"] == [1, 2.5, None]
finally:
os.unlink(tmppath)
def test_metadata_item_assignment_rejects_non_json_on_write(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0)],
)
frame.metadata["bad"] = object()
with pytest.raises((TypeError, ValueError), match="metadata|JSON"):
readcon.write_con_string([frame])
def test_atoms_live_list_mutations_persist_through_write(self):
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=[readcon.Atom(symbol="H", x=0.0, y=0.0, z=0.0, atom_id=0, mass=1.008)],
)
atoms = frame.atoms
atoms.append(readcon.Atom(symbol="Cu", x=1.0, y=1.0, z=1.0, atom_id=1, mass=63.546))
atoms[0] = readcon.Atom(symbol="He", x=2.0, y=2.0, z=2.0, atom_id=0, mass=4.0026)
atoms[1].x = 4.5
reread = readcon.read_con_string(readcon.write_con_string([frame]))[0]
assert len(reread) == 2
assert [atom.symbol for atom in reread.atoms] == ["He", "Cu"]
assert reread.atoms[0].x == pytest.approx(2.0)
assert reread.atoms[1].x == pytest.approx(4.5)
assert reread.atoms[1].mass == pytest.approx(63.546, abs=0.01)
def test_read_first_frame_and_iter_con(self):
path = _resource("tiny_multi_cuh2.con")
first = readcon.read_first_frame(path)
assert len(first) == 4
assert first.atoms[0].symbol == "Cu"
iterator = readcon.iter_con(path)
assert iter(iterator) is iterator
frames = list(iterator)
assert len(frames) == 2
assert [len(frame) for frame in frames] == [4, 4]
class TestMass:
def test_mass_from_file(self):
frames = readcon.read_con(_resource("tiny_cuh2.con"))
cu_atom = frames[0].atoms[0]
assert cu_atom.mass is not None
assert cu_atom.mass == pytest.approx(63.546, abs=0.01)
def test_mass_roundtrip(self):
atoms = [
readcon.Atom(symbol="Pt", x=0.0, y=0.0, z=0.0, mass=195.08),
]
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=atoms,
)
output = readcon.write_con_string([frame])
frames2 = readcon.read_con_string(output)
assert frames2[0].atoms[0].mass == pytest.approx(195.08, abs=0.01)
class TestPrecision:
def test_default_precision_6(self):
atoms = [
readcon.Atom(symbol="Cu", x=1.23456789012345, y=0.0, z=0.0),
]
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=atoms,
)
output = readcon.write_con_string([frame])
frames2 = readcon.read_con_string(output)
assert frames2[0].atoms[0].x == pytest.approx(1.234568, abs=1e-6)
def test_high_precision_17(self):
atoms = [
readcon.Atom(symbol="Cu", x=1.23456789012345, y=0.0, z=0.0),
]
frame = readcon.ConFrame(
cell=[10.0, 10.0, 10.0],
angles=[90.0, 90.0, 90.0],
atoms=atoms,
)
output = readcon.write_con_string([frame], precision=17)
frames2 = readcon.read_con_string(output)
assert frames2[0].atoms[0].x == pytest.approx(1.23456789012345, abs=1e-14)
class TestNumpyArrays:
def test_coords_array_shape(self):
np = pytest.importorskip("numpy")
frame = readcon.read_con(_resource("tiny_cuh2.con"))[0]
coords = frame.coords_array()
assert coords.shape == (len(frame), 3)
assert coords.dtype == np.float64
assert coords[0, 0] == pytest.approx(frame.atoms[0].x)
def test_velocities_array_returns_none_without_velocities(self):
frame = readcon.read_con(_resource("tiny_cuh2.con"))[0]
assert frame.velocities_array() is None
def test_forces_array_round_trips(self):
np = pytest.importorskip("numpy")
frame = readcon.read_con(_resource("tiny_cuh2_forces.con"))[0]
forces = frame.forces_array()
assert forces is not None
assert forces.shape == (len(frame), 3)
assert forces[0, 0] == pytest.approx(frame.atoms[0].fx)
def test_atom_ids_array(self):
np = pytest.importorskip("numpy")
frame = readcon.read_con(_resource("tiny_cuh2.con"))[0]
ids = frame.atom_ids_array()
assert ids.dtype == np.uint64
assert ids.shape == (len(frame),)
def test_build_atom_id_index(self):
frame = readcon.read_con(_resource("tiny_cuh2.con"))[0]
idx = frame.build_atom_id_index()
assert isinstance(idx, dict)
assert len(idx) == len(frame)
for atom_id, position in idx.items():
assert frame.atoms[position].atom_id == atom_id
class TestErrorHandling:
def test_bad_file_path(self):
with pytest.raises(OSError):
readcon.read_con("/nonexistent/path.con")
def test_malformed_data(self):
with pytest.raises(OSError):
readcon.read_con_string("not a valid con file\n")