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update analysis unit tests so that they check results against some ge…
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…nerated reference values
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@ChiCheng45
ChiCheng45 committed Jan 28, 2025
1 parent df2fb58 commit 7aa2f46
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Showing 70 changed files with 465 additions and 93 deletions.
2 changes: 1 addition & 1 deletion MDANSE/Tests/UnitTests/Analysis/test_average_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def trajectory():


@pytest.mark.parametrize("output_unit,output_format", inputs)
def test_temperature(trajectory, output_unit, output_format):
def test_avg_structure(trajectory, output_unit, output_format):
temp_name = tempfile.mktemp()
parameters = {}
parameters["frames"] = (0, 10, 1)
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164 changes: 151 additions & 13 deletions MDANSE/Tests/UnitTests/Analysis/test_dynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@
import tempfile
import os
from os import path

import h5py
import numpy as np
import pytest

from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
Expand All @@ -15,13 +18,17 @@
"Data",
"short_trajectory_after_changes.mdt",
)

mdmc_traj = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"..",
"Data",
"Ar_mdmc_h5md.h5",
)
result_dir = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"..",
"Results",
)


@pytest.fixture(scope="module")
Expand Down Expand Up @@ -54,6 +61,20 @@ def test_vacf(trajectory, interp_order, normalise):
vacf.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")

if normalise:
fname = f"vacf_{interp_order}_normalised.mda"
else:
fname = f"vacf_{interp_order}.mda"

result_file = os.path.join(result_dir, fname)

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
np.testing.assert_array_almost_equal(actual["/vacf_Cu"], desired["/vacf_Cu"])
np.testing.assert_array_almost_equal(actual["/vacf_S"], desired["/vacf_S"])
np.testing.assert_array_almost_equal(actual["/vacf_Sb"], desired["/vacf_Sb"])
np.testing.assert_array_almost_equal(actual["/vacf_total"], desired["/vacf_total"])

os.remove(temp_name + ".mda")
assert path.exists(temp_name + ".log")
assert path.isfile(temp_name + ".log")
Expand All @@ -71,6 +92,19 @@ def test_pps(trajectory):
pps.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")

result_file = os.path.join(result_dir, "pps.mda")

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
np.testing.assert_array_almost_equal(actual["/pacf_Cu"], desired["/pacf_Cu"])
np.testing.assert_array_almost_equal(actual["/pacf_S"], desired["/pacf_S"])
np.testing.assert_array_almost_equal(actual["/pacf_Sb"], desired["/pacf_Sb"])
np.testing.assert_array_almost_equal(actual["/pacf_total"], desired["/pacf_total"])
np.testing.assert_array_almost_equal(actual["/pps_Cu"], desired["/pps_Cu"])
np.testing.assert_array_almost_equal(actual["/pps_S"], desired["/pps_S"])
np.testing.assert_array_almost_equal(actual["/pps_Sb"], desired["/pps_Sb"])
np.testing.assert_array_almost_equal(actual["/pps_total"], desired["/pps_total"])

os.remove(temp_name + ".mda")
assert path.exists(temp_name + ".log")
assert path.isfile(temp_name + ".log")
Expand Down Expand Up @@ -112,37 +146,141 @@ def parameters():

total_list = []

for tp in [short_traj, mdmc_traj]:
for tp in [("short_traj", short_traj), ("mdmc_traj", mdmc_traj)]:
for jt in [
# "AngularCorrelation",
# "GeneralAutoCorrelationFunction",
"CurrentCorrelationFunction",
"DensityOfStates",
"MeanSquareDisplacement",
"VelocityAutoCorrelationFunction",
"VanHoveFunctionDistinct",
"VanHoveFunctionSelf",
("DensityOfStates", {
"mdmc_traj": [
"dos_Ar",
"dos_total",
"vacf_Ar",
"vacf_total"
],
"short_traj": [
"dos_Cu",
"dos_S",
"dos_Sb",
"dos_total",
"vacf_Cu",
"vacf_S",
"vacf_Sb",
"vacf_total",
]
}),
("MeanSquareDisplacement", {
"mdmc_traj": [
"msd_Ar",
"msd_total",
],
"short_traj": [
"msd_Cu",
"msd_S",
"msd_Sb",
"msd_total",
]
}),
("VelocityAutoCorrelationFunction", {
"mdmc_traj": [
"vacf_Ar",
"vacf_total"
],
"short_traj": [
"vacf_Cu",
"vacf_S",
"vacf_Sb",
"vacf_total",
]
}),
("VanHoveFunctionDistinct", {
"mdmc_traj": [
"g(r,t)_inter_ArAr",
"g(r,t)_inter_total",
"g(r,t)_intra_ArAr",
"g(r,t)_intra_total",
"g(r,t)_total",
"g(r,t)_total_ArAr",
],
"short_traj": [
"g(r,t)_inter_CuCu",
"g(r,t)_inter_CuS",
"g(r,t)_inter_CuSb",
"g(r,t)_inter_SS",
"g(r,t)_inter_SSb",
"g(r,t)_inter_SbSb",
"g(r,t)_inter_total",
"g(r,t)_intra_CuCu",
"g(r,t)_intra_CuS",
"g(r,t)_intra_CuSb",
"g(r,t)_intra_SS",
"g(r,t)_intra_SSb",
"g(r,t)_intra_SbSb",
"g(r,t)_intra_total",
"g(r,t)_total_CuCu",
"g(r,t)_total_CuS",
"g(r,t)_total_CuSb",
"g(r,t)_total_SS",
"g(r,t)_total_SSb",
"g(r,t)_total_SbSb",
"g(r,t)_total",
]
}),
("VanHoveFunctionSelf", {
"mdmc_traj": [
"4_pi_r2_g(r,t)_Ar",
"4_pi_r2_g(r,t)_total",
"g(r,t)_Ar",
"g(r,t)_total",
],
"short_traj": [
"4_pi_r2_g(r,t)_Cu",
"4_pi_r2_g(r,t)_S",
"4_pi_r2_g(r,t)_Sb",
"4_pi_r2_g(r,t)_total",
"g(r,t)_Cu",
"g(r,t)_S",
"g(r,t)_Sb",
"g(r,t)_total",
]
}),
# "OrderParameter",
"PositionAutoCorrelationFunction",
("PositionAutoCorrelationFunction", {
"mdmc_traj": [
"pacf_Ar",
"pacf_total"
],
"short_traj": [
"pacf_Cu",
"pacf_S",
"pacf_Sb",
"pacf_total",
]
}),
]:
for rm in [("single-core", 1), ("multicore", -4)]:
for of in ["MDAFormat", "TextFormat"]:
total_list.append((tp, jt, rm, of))


@pytest.mark.parametrize("traj_path,job_type,running_mode,output_format", total_list)
@pytest.mark.parametrize("traj_info,job_info,running_mode,output_format", total_list)
def test_dynamics_analysis(
parameters, traj_path, job_type, running_mode, output_format
parameters, traj_info, job_info, running_mode, output_format
):
temp_name = tempfile.mktemp()
parameters["trajectory"] = traj_path
parameters["trajectory"] = traj_info[1]
parameters["running_mode"] = running_mode
parameters["output_files"] = (temp_name, (output_format,), "INFO")
job = IJob.create(job_type)
job = IJob.create(job_info[0])
job.run(parameters, status=True)
if output_format == "MDAFormat":
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
result_file = os.path.join(result_dir, f"dynamics_analysis_{traj_info[0]}_{job_info[0]}.mda")

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
for key in job_info[1][traj_info[0]]:
np.testing.assert_array_almost_equal(actual[f"/{key}"], desired[f"/{key}"])

os.remove(temp_name + ".mda")
elif output_format == "TextFormat":
assert path.exists(temp_name + "_text.tar")
Expand Down
51 changes: 49 additions & 2 deletions MDANSE/Tests/UnitTests/Analysis/test_infrared.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,9 @@
import os
from os import path

import h5py
import numpy as np

from MDANSE.Framework.Jobs.IJob import IJob


Expand All @@ -14,6 +17,11 @@
"Data",
"named_molecules.mdt",
)
result_dir = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"..",
"Results",
)


def test_dacf_analysis():
Expand All @@ -23,13 +31,32 @@ def test_dacf_analysis():
parameters["output_files"] = (temp_name, ("MDAFormat",), "INFO")
parameters["running_mode"] = ("single-core", 1)
parameters["trajectory"] = short_traj
parameters["atom_charges"] = "{}"
parameters["atom_charges"] = (
'{"0": 0.72, "1": -0.36, "2": -0.36, "3": 0.72, "4": -0.36, '
'"5": -0.36, "6": 0.72, "7": -0.36, "8": -0.36, "9": 0.72, '
'"10": -0.36, "11": -0.36, "12": 0.72, "13": -0.36, "14": -0.36, '
'"15": 0.72, "16": -0.36, "17": -0.36, "18": 0.72, "19": -0.36, '
'"20": -0.36, "21": 0.72, "22": -0.36, "23": -0.36, "24": 0.72, '
'"25": -0.36, "26": -0.36, "27": 0.72, "28": -0.36, "29": -0.36, '
'"30": 0.72, "31": -0.36, "32": -0.36, "33": 0.72, "34": -0.36, '
'"35": -0.36, "36": 0.72, "37": -0.36, "38": -0.36, "39": 0.72, '
'"40": -0.36, "41": -0.36, "42": 0.72, "43": -0.36, "44": -0.36, '
'"45": 0.72, "46": -0.36, "47": -0.36, "48": 0.72, "49": -0.36, '
'"50": -0.36, "51": 0.72, "52": -0.36, "53": -0.36, "54": 0.72, '
'"55": -0.36, "56": -0.36, "57": 0.72, "58": -0.36, "59": -0.36}'
)
parameters["molecule_name"] = "InChI=1S/CO2/c2-1-3"
job = IJob.create("DipoleAutoCorrelationFunction")
job.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
result_file = os.path.join(result_dir, "dacf_analysis.mda")

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
np.testing.assert_array_almost_equal(actual["/dacf"], desired["/dacf"])

os.remove(temp_name + ".mda")

assert path.exists(temp_name + ".log")
assert path.isfile(temp_name + ".log")
os.remove(temp_name + ".log")
Expand All @@ -44,13 +71,33 @@ def test_ir_analysis():
parameters["derivative_order"] = 3
parameters["running_mode"] = ("single-core", 1)
parameters["trajectory"] = short_traj
parameters["atom_charges"] = "{}"
parameters["atom_charges"] = (
'{"0": 0.72, "1": -0.36, "2": -0.36, "3": 0.72, "4": -0.36, '
'"5": -0.36, "6": 0.72, "7": -0.36, "8": -0.36, "9": 0.72, '
'"10": -0.36, "11": -0.36, "12": 0.72, "13": -0.36, "14": -0.36, '
'"15": 0.72, "16": -0.36, "17": -0.36, "18": 0.72, "19": -0.36, '
'"20": -0.36, "21": 0.72, "22": -0.36, "23": -0.36, "24": 0.72, '
'"25": -0.36, "26": -0.36, "27": 0.72, "28": -0.36, "29": -0.36, '
'"30": 0.72, "31": -0.36, "32": -0.36, "33": 0.72, "34": -0.36, '
'"35": -0.36, "36": 0.72, "37": -0.36, "38": -0.36, "39": 0.72, '
'"40": -0.36, "41": -0.36, "42": 0.72, "43": -0.36, "44": -0.36, '
'"45": 0.72, "46": -0.36, "47": -0.36, "48": 0.72, "49": -0.36, '
'"50": -0.36, "51": 0.72, "52": -0.36, "53": -0.36, "54": 0.72, '
'"55": -0.36, "56": -0.36, "57": 0.72, "58": -0.36, "59": -0.36}'
)
parameters["molecule_name"] = "InChI=1S/CO2/c2-1-3"
job = IJob.create("Infrared")
job.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
result_file = os.path.join(result_dir, "ir_analysis.mda")

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
np.testing.assert_array_almost_equal(actual["/ddacf"], desired["/ddacf"])
np.testing.assert_array_almost_equal(actual["/ir"], desired["/ir"])

os.remove(temp_name + ".mda")

assert path.exists(temp_name + ".log")
assert path.isfile(temp_name + ".log")
os.remove(temp_name + ".log")
22 changes: 16 additions & 6 deletions MDANSE/Tests/UnitTests/Analysis/test_mdmc_h5md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,11 @@
"Data",
"Ar_mdmc_h5md.h5",
)
result_dir = os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"..",
"Results",
)


@pytest.fixture(scope="module")
Expand All @@ -25,22 +30,27 @@ def trajectory():


@pytest.mark.parametrize("interp_order", [1, 3])
def test_temperature_nonzero(trajectory, interp_order):
def test_h5md_temperature(trajectory, interp_order):
pos = trajectory._data.coordinates(0)
print(f"Coordinates span: {pos.min()}, {pos.max()}")
print(f"Trajectory length: {len(trajectory.trajectory)}")
print(f"Positions array shape: {trajectory.trajectory.variable('position').shape}")
temp_name = tempfile.mktemp()
parameters = {}
parameters["frames"] = (0, 10, 1)
parameters["frames"] = (0, 39, 1)
parameters["interpolation_order"] = interp_order
parameters["output_files"] = (temp_name, ("MDAFormat",), "INFO")
parameters["running_mode"] = ("single-core",)
parameters["trajectory"] = short_traj
temp = IJob.create("Temperature")
temp.run(parameters, status=True)
with h5py.File(temp_name + ".mda") as results:
print(results.keys())
temperature = np.array(results["/temperature"])
result_file = os.path.join(
result_dir, f"h5md_temperature_{interp_order}.mda")

with h5py.File(temp_name + ".mda") as actual, h5py.File(result_file) as desired:
np.testing.assert_array_almost_equal(actual["/kinetic_energy"], desired["/kinetic_energy"])
np.testing.assert_array_almost_equal(actual["/temperature"], desired["/temperature"])
np.testing.assert_array_almost_equal(actual["/avg_kinetic_energy"], desired["/avg_kinetic_energy"])
np.testing.assert_array_almost_equal(actual["/avg_temperature"], desired["/avg_temperature"])

os.remove(temp_name + ".mda")
assert np.all(temperature > 0.0)
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