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fixed path of test_files to work with new package structure
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@FrederikLizakJohansen
FrederikLizakJohansen committed Aug 28, 2024
1 parent 7bb25e5 commit 56d3915
Showing 1 changed file with 28 additions and 26 deletions.
54 changes: 28 additions & 26 deletions debyecalculator/test_debye_calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ def test_iq_cif():

# Calculate the scatering intensity using DebyeCalculator
calc.update_parameters(qstep=0.05)
q, iq = calc.iq('data/AntiFluorite_Co2O.cif', radii=10.0)
q, iq = calc.iq('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)

# Normalise counts
eps = 1e-16
Expand Down Expand Up @@ -126,7 +126,7 @@ def test_sq_cif():

# Calculate the structure factor using the DebyeCalculator
calc.update_parameters(qstep=0.05)
q, sq = calc.sq('data/AntiFluorite_Co2O.cif', radii=10.0)
q, sq = calc.sq('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)

# Check that the calculated structure factor matches the expected value
assert np.allclose(q, q_expected, atol=1e-04, rtol=1e-03), f"Expected Q to be {q_expected}, but got {q}"
Expand Down Expand Up @@ -173,7 +173,7 @@ def test_fq_cif():

# Calculate the structure factor using the DebyeCalculator
calc.update_parameters(qstep=0.05)
q, fq = calc.fq('data/AntiFluorite_Co2O.cif', radii=10.0)
q, fq = calc.fq('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)

# Check that the calculated structure factor matches the expected value
assert np.allclose(q, q_expected, atol=1e-04, rtol=1e-03), f"Expected Q to be {q_expected}, but got {q}"
Expand Down Expand Up @@ -220,7 +220,7 @@ def test_gr_cif():

# Calculate the structure factor using the DebyeCalculator
calc.update_parameters(qstep=0.05)
r, gr = calc.gr('data/AntiFluorite_Co2O.cif', radii=10.0)
r, gr = calc.gr('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)

# Check that the calculated structure factor matches the expected value
assert np.allclose(r, r_expected, atol=1e-04, rtol=1e-03), f"Expected r to be {r_expected}, but got {r}"
Expand Down Expand Up @@ -286,7 +286,7 @@ def test_get_all_cif():

# Calculate Iq, Fq, Sq, and Gr using the DebyeCalculator
calc.update_parameters(qstep=0.05)
r, q, iq, sq, fq, gr = calc._get_all('data/AntiFluorite_Co2O.cif', radii=10.0)
r, q, iq, sq, fq, gr = calc._get_all('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)

# Check that the calculated Iq matches the expected value
ph = np.genfromtxt('debyecalculator/unittests_files/iq_AntiFluorite_Co2O_radius10.0.dat', delimiter=',', skip_header=15)
Expand Down Expand Up @@ -375,39 +375,41 @@ def test_partials():
"""
Testing whether the partials add up
"""
cif_path = "debyecalculator/data/AntiFluorite_Co2O.cif"

# I(Q)
_, iq = calc.iq("data/AntiFluorite_Co2O.cif", radii=5, partial=None)
_, iq_o_o = calc.iq("data/AntiFluorite_Co2O.cif", radii=5, partial="O-O", include_self_scattering=True)
_, iq_co_o = calc.iq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-O", include_self_scattering=False)
_, iq_co_co = calc.iq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-Co", include_self_scattering=True)
_, iq = calc.iq(cif_path, radii=5, partial=None)
_, iq_o_o = calc.iq(cif_path, radii=5, partial="O-O", include_self_scattering=True)
_, iq_co_o = calc.iq(cif_path, radii=5, partial="Co-O", include_self_scattering=False)
_, iq_co_co = calc.iq(cif_path, radii=5, partial="Co-Co", include_self_scattering=True)
iq_added = iq_o_o + iq_co_o + iq_co_co
assert np.allclose(iq, iq_added, atol=1e-04, rtol=1e-03), f"Partials are not matching for I(Q) calculations"
# S(Q)
_, sq = calc.sq("data/AntiFluorite_Co2O.cif", radii=5, partial=None)
_, sq_o_o = calc.sq("data/AntiFluorite_Co2O.cif", radii=5, partial="O-O", )
_, sq_co_o = calc.sq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-O", )
_, sq_co_co = calc.sq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-Co", )
_, sq = calc.sq(cif_path, radii=5, partial=None)
_, sq_o_o = calc.sq(cif_path, radii=5, partial="O-O", )
_, sq_co_o = calc.sq(cif_path, radii=5, partial="Co-O", )
_, sq_co_co = calc.sq(cif_path, radii=5, partial="Co-Co", )
sq_added = sq_o_o + sq_co_o + sq_co_co
assert np.allclose(sq, sq_added, atol=1e-04, rtol=1e-03), f"Partials are not matching for S(Q) calculations"
# F(Q)
_, fq = calc.fq("data/AntiFluorite_Co2O.cif", radii=5, partial=None)
_, fq_o_o = calc.fq("data/AntiFluorite_Co2O.cif", radii=5, partial="O-O", )
_, fq_co_o = calc.fq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-O", )
_, fq_co_co = calc.fq("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-Co", )
_, fq = calc.fq(cif_path, radii=5, partial=None)
_, fq_o_o = calc.fq(cif_path, radii=5, partial="O-O", )
_, fq_co_o = calc.fq(cif_path, radii=5, partial="Co-O", )
_, fq_co_co = calc.fq(cif_path, radii=5, partial="Co-Co", )
fq_added = fq_o_o + fq_co_o + fq_co_co
assert np.allclose(fq, fq_added, atol=1e-04, rtol=1e-03), f"Partials are not matching for F(Q) calculations"
# G(r)
_, gr = calc.gr("data/AntiFluorite_Co2O.cif", radii=5, partial=None)
_, gr_o_o = calc.gr("data/AntiFluorite_Co2O.cif", radii=5, partial="O-O", )
_, gr_co_o = calc.gr("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-O", )
_, gr_co_co = calc.gr("data/AntiFluorite_Co2O.cif", radii=5, partial="Co-Co", )
_, gr = calc.gr(cif_path, radii=5, partial=None)
_, gr_o_o = calc.gr(cif_path, radii=5, partial="O-O", )
_, gr_co_o = calc.gr(cif_path, radii=5, partial="Co-O", )
_, gr_co_co = calc.gr(cif_path, radii=5, partial="Co-Co", )
gr_added = gr_o_o + gr_co_o + gr_co_co
assert np.allclose(gr, gr_added, atol=1e-04, rtol=1e-03), f"Partials are not matching for G(r) calculations"
# _get_all
_, _, iq, sq, fq, gr = calc._get_all('data/AntiFluorite_Co2O.cif', radii=5, partial=None)
_, _, iq_o_o, sq_o_o, fq_o_o, gr_o_o = calc._get_all('data/AntiFluorite_Co2O.cif', radii=5, partial="O-O", include_self_scattering=True)
_, _, iq_co_o, sq_co_o, fq_co_o, gr_co_o = calc._get_all('data/AntiFluorite_Co2O.cif', radii=5, partial="Co-O", include_self_scattering=False)
_, _, iq_co_co, sq_co_co, fq_co_co, gr_co_co = calc._get_all('data/AntiFluorite_Co2O.cif', radii=5, partial="Co-Co", include_self_scattering=True)
_, _, iq, sq, fq, gr = calc._get_all(cif_path, radii=5, partial=None)
_, _, iq_o_o, sq_o_o, fq_o_o, gr_o_o = calc._get_all(cif_path, radii=5, partial="O-O", include_self_scattering=True)
_, _, iq_co_o, sq_co_o, fq_co_o, gr_co_o = calc._get_all(cif_path, radii=5, partial="Co-O", include_self_scattering=False)
_, _, iq_co_co, sq_co_co, fq_co_co, gr_co_co = calc._get_all(cif_path, radii=5, partial="Co-Co", include_self_scattering=True)
iq_added = iq_o_o + iq_co_o + iq_co_co
assert np.allclose(iq, iq_added, atol=1e-04, rtol=1e-03), f"Partials are not matching for I(Q) calculations"
sq_added = sq_o_o + sq_co_o + sq_co_co
Expand All @@ -425,7 +427,7 @@ def test_generate_nanoparticle():
elements = ase_structure.get_chemical_symbols()

# Generate xyz from utility function
structure = generate_nanoparticles('data/AntiFluorite_Co2O.cif', radii=10.0)[0]
structure = generate_nanoparticles('debyecalculator/data/AntiFluorite_Co2O.cif', radii=10.0)[0]

# Assert
assert np.allclose(xyz, structure.xyz.cpu(), atol=1e-04, rtol=1e-03), f"Expected xyz to be {xyz}, but got {structure.xyz}"
Expand Down

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