1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
from pathlib import Path
import numpy as np
from emmet.core.openmm.tasks import CalculationOutput
def test_calc_output_from_directory(test_dir):
output_dir = test_dir / "openmm" / "calc_output"
# Call the from_directory function
calc_out = CalculationOutput.from_directory(
output_dir,
"state.csv",
"trajectory.dcd",
elapsed_time=10.0,
)
# Assert the expected attributes of the CalculationOutput object
assert isinstance(calc_out, CalculationOutput)
assert calc_out.dir_name == str(output_dir)
assert calc_out.elapsed_time == 10.0
assert calc_out.traj_file == "trajectory.dcd"
assert calc_out.state_file == "state.csv"
# Assert the contents of the state data
assert np.array_equal(calc_out.steps_reported[:3], [100, 200, 300])
assert np.allclose(calc_out.potential_energy[:3], [-26192.4, -25648.6, -25149.6])
assert np.allclose(calc_out.kinetic_energy[:3], [609.4, 1110.4, 1576.4], atol=0.1)
assert np.allclose(calc_out.total_energy[:3], [-25583.1, -24538.1, -23573.2])
assert np.allclose(calc_out.temperature[:3], [29.6, 54.0, 76.6], atol=0.1)
assert np.allclose(calc_out.volume[:3], [21.9, 21.9, 21.9], atol=0.1)
assert np.allclose(calc_out.density[:3], [1.0, 0.99, 0.99], atol=0.1)
# Assert the existence of the DCD and state files
assert Path(calc_out.dir_name, calc_out.traj_file).exists()
assert Path(calc_out.dir_name, calc_out.state_file).exists()
|
