CI/integration_tests/calculators/test_einstein_distinct_diffusion_coefficients.py
"""
MDSuite: A Zincwarecode package.
License
-------
This program and the accompanying materials are made available under the terms
of the Eclipse Public License v2.0 which accompanies this distribution, and is
available at https://www.eclipse.org/legal/epl-v20.html
SPDX-License-Identifier: EPL-2.0
Copyright Contributors to the Zincwarecode Project.
Contact Information
-------------------
email: zincwarecode@gmail.com
github: https://github.com/zincware
web: https://zincwarecode.com/
Citation
--------
If you use this module please cite us with:
Summary
-------
Test the einstein distinct diffusion coefficient module.
Notes
-----
Currently this test only checks that these calculators actually run it does not compare
values.
"""
import os
import pytest
from zinchub import DataHub
import mdsuite as mds
@pytest.fixture(scope="session")
def traj_file(tmp_path_factory) -> str:
"""Download trajectory file into a temporary directory and keep it for all tests."""
temporary_path = tmp_path_factory.getbasetemp()
NaCl = DataHub(
url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
)
NaCl.get_file(path=temporary_path)
return (temporary_path / NaCl.file_raw).as_posix()
@pytest.fixture(scope="session")
def true_values() -> dict:
"""Example fixture for downloading analysis results from github."""
NaCl = DataHub(
url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
)
return NaCl.get_analysis(analysis="RadialDistributionFunction.json")
@pytest.mark.parametrize("desired_memory", (None, 0.001))
def test_eddc_project(traj_file, true_values, tmp_path, desired_memory):
"""Test the EinsteinDistinctDiffusionCoefficients called from the project class."""
with mds.utils.helpers.change_memory_fraction(desired_memory=desired_memory):
os.chdir(tmp_path)
project = mds.Project()
project.add_experiment(
"NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
)
project.run.EinsteinDistinctDiffusionCoefficients(
plot=False, data_range=300, correlation_time=100
)
# data_dict = project.load.EinsteinDistinctDiffusionCoefficients()[0].data_dict
#
# data = Path(
# r"C:\Users\fabia\Nextcloud\DATA\JupyterProjects\MDSuite\CI\integration_tests"
# r"\calculators\data\einstein_distinct_diffusion_coefficients.json"
# )
#
# data.write_text(json.dumps(data_dict))
#
# np.testing.assert_array_almost_equal(data_dict["x"], true_values["x"])
# np.testing.assert_array_almost_equal(
# data_dict["uncertainty"], true_values["uncertainty"]
# )
def test_eddc_experiment(traj_file, true_values, tmp_path):
"""Test the EinsteinDistinctDiffusionCoefficients called from the experiment class."""
os.chdir(tmp_path)
project = mds.Project()
project.add_experiment(
"NaCl", simulation_data=traj_file, timestep=0.002, temperature=1400
)
project.experiments["NaCl"].run.EinsteinDiffusionCoefficients(
plot=False, data_range=300, correlation_time=100
)