def test_replicate_gp():
"""
Based on gp_test_al.out, ensures that given hyperparameters and DFT calls
a GP model can be reproduced and correctly re-predict forces and
uncertainties
:return:
"""
os.system('cp test_files/sample_h2_otf.out .')
parsed = OtfAnalysis('sample_h2_otf.out')
positions = parsed.position_list
forces = parsed.force_list
gp_model = parsed.make_gp()
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
final_structure = structures[-1]
pred_for, pred_stds = predict_on_structure(final_structure, gp_model)
assert np.isclose(final_structure.forces, pred_for).all()
assert np.isclose(final_structure.stds, pred_stds).all()
set_of_structures = structures[-3:-1]
for structure in set_of_structures:
pred_for, pred_stds = predict_on_structure(structure, gp_model)
assert np.isclose(structure.forces, pred_for, atol=1e-6).all()
assert np.isclose(structure.stds, pred_stds, atol=1e-6).all()
os.system('rm sample_slab_otf.out')
def test_replicate_gp():
"""
Based on gp_test_al.out, ensures that given hyperparameters and DFT calls
a GP model can be reproduced and correctly re-predict forces and
uncertainties
:return:
"""
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
positions = parsed.position_list
forces = parsed.force_list
gp_model = parsed.make_gp(kernel_name="two_plus_three_body_mc")
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
final_structure = structures[-1]
pred_for, pred_stds = predict_on_structure(final_structure, gp_model)
assert np.isclose(final_structure.forces, pred_for, rtol=1e-3).all()
assert np.isclose(final_structure.stds, pred_stds, rtol=1e-3).all()
set_of_structures = structures[-3:-1]
for structure in set_of_structures:
pred_for, pred_stds = predict_on_structure(structure, gp_model)
assert np.isclose(structure.forces, pred_for, rtol=1e-3,
atol=1e-6).all()
assert np.isclose(structure.stds, pred_stds, rtol=1e-3,
atol=1e-6).all()
def test_output_md_structures():
parsed = OtfAnalysis('test_files/VelocityVerlet.log')
positions = parsed.position_list
forces = parsed.force_list
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()
def test_output_md_structures():
os.system('cp test_files/sample_slab_otf.out .')
parsed = OtfAnalysis('sample_slab_otf.out')
positions = parsed.position_list
forces = parsed.force_list
structures = parsed.output_md_structures()
assert np.isclose(structures[-1].positions, positions[-1]).all()
assert np.isclose(structures[-1].forces, forces[-1]).all()