Update analysis and converter unit tests so they check against reference values

MDANSE/Src/MDANSE/Framework/Converters/DCD.py

@@ -360,7 +360,7 @@ def run_step(self, index):
             conf.fold_coordinates()
 
         # The current time.
-        time = (index + 1) * self.configuration["time_step"]["value"]
+        time = index * self.configuration["time_step"]["value"]
 
         # Store a snapshot of the current configuration in the output trajectory.
         self._trajectory.dump_configuration(

MDANSE/Tests/UnitTests/Analysis/test_average_structure.py

@@ -1,4 +1,3 @@
-import sys
 import tempfile
 import os
 from os import path
@@ -8,11 +7,10 @@
 from MDANSE.Framework.Jobs.IJob import IJob
 
 
-sys.setrecursionlimit(100000)
 short_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "short_trajectory_after_changes.mdt",
 )
 
@@ -32,7 +30,7 @@ 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)

MDANSE/Tests/UnitTests/Analysis/test_dynamics.py

@@ -1,34 +1,37 @@
-import sys
 import tempfile
 import os
 from os import path
+
+import h5py
+import numpy as np
 import pytest
 
-from MDANSE.Framework.InputData.HDFTrajectoryInputData import HDFTrajectoryInputData
 from MDANSE.Framework.Jobs.IJob import IJob
 
 
-sys.setrecursionlimit(100000)
 short_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "short_trajectory_after_changes.mdt",
 )
-
 mdmc_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "Ar_mdmc_h5md.h5",
 )
-
 com_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "com_trajectory.mdt",
 )
+result_dir = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)),
+    "..",
+    "Results",
+)
 
 
 @pytest.mark.parametrize(
@@ -55,6 +58,20 @@ def test_vacf(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")
@@ -72,6 +89,19 @@ def test_pps():
     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")
@@ -99,7 +129,7 @@ def parameters():
         },
     )
     parameters["q_values"] = (0.0, 10.0, 0.1)
-    parameters["r_values"] = (0.0, 0.5, 0.01)
+    parameters["r_values"] = (0.0, 0.9, 0.01)
     parameters["per_axis"] = False
     parameters["reference_direction"] = (0, 0, 1)
     parameters["instrument_resolution"] = ("Gaussian", {"sigma": 1.0, "mu": 0.0})
@@ -113,37 +143,43 @@ def parameters():
 
 total_list = []
 
-for tp in [short_traj, mdmc_traj, com_traj]:
+for tp in [("short_traj", short_traj), ("mdmc_traj", mdmc_traj), ("com_traj", com_traj)]:
     for jt in [
         # "AngularCorrelation",
         # "GeneralAutoCorrelationFunction",
-        "CurrentCorrelationFunction",
-        "DensityOfStates",
-        "MeanSquareDisplacement",
-        "VelocityAutoCorrelationFunction",
-        "VanHoveFunctionDistinct",
-        "VanHoveFunctionSelf",
+        ("DensityOfStates", ["dos", "vacf"]),
+        ("MeanSquareDisplacement", ["msd"]),
+        ("VelocityAutoCorrelationFunction", ["vacf"]),
+        ("VanHoveFunctionDistinct", ["g(r,t)"]),
+        ("VanHoveFunctionSelf", ["g(r,t)"]),
         # "OrderParameter",
-        "PositionAutoCorrelationFunction",
+        ("PositionAutoCorrelationFunction", ["pacf"]),
     ]:
         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:
+            keys = [i for i in desired.keys() if any([j in i for j in job_info[1]])]
+            for key in keys:
+                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")

MDANSE/Tests/UnitTests/Analysis/test_infrared.py

@@ -1,19 +1,24 @@
-import sys
 import tempfile
 import os
 from os import path
 
-from MDANSE.Framework.Jobs.IJob import IJob
+import h5py
+import numpy as np
 
+from MDANSE.Framework.Jobs.IJob import IJob
 
-sys.setrecursionlimit(100000)
 
 short_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "named_molecules.mdt",
 )
+result_dir = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)),
+    "..",
+    "Results",
+)
 
 
 def test_dacf_analysis():
@@ -23,13 +28,32 @@ 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"] = "C1_O2"
     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")
@@ -44,13 +68,33 @@ 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"] = "C1_O2"
     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")

MDANSE/Tests/UnitTests/Analysis/test_mcstas.py

@@ -1,4 +1,3 @@
-import sys
 import tempfile
 import os
 from os import path
@@ -7,12 +6,10 @@
 from MDANSE.Framework.Jobs.IJob import IJob
 
 
-sys.setrecursionlimit(100000)
-
 short_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "short_trajectory_after_changes.mdt",
 )
 

MDANSE/Tests/UnitTests/Analysis/test_mdmc_h5md.py

@@ -1,4 +1,3 @@
-import sys
 import tempfile
 import os
 import pytest
@@ -9,13 +8,17 @@
 from MDANSE.Framework.Jobs.IJob import IJob
 
 
-sys.setrecursionlimit(100000)
 short_traj = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     "..",
-    "Data",
+    "Converted",
     "Ar_mdmc_h5md.h5",
 )
+result_dir = os.path.join(
+    os.path.dirname(os.path.realpath(__file__)),
+    "..",
+    "Results",
+)
 
 
 @pytest.fixture(scope="module")
@@ -25,22 +28,27 @@ 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)