Make VACF test work with MockTrajectory

MDANSE/Src/MDANSE/Framework/Configurable.py

@@ -42,7 +42,7 @@ class Configurable(object):
 
     settings = collections.OrderedDict()
 
-    def __init__(self, settings=None, mdmc_input_override=False):
+    def __init__(self, settings=None, trajectory_input="mdasne"):
         """
         Constructor
         """
@@ -56,17 +56,28 @@ def __init__(self, settings=None, mdmc_input_override=False):
         if settings is not None:
             self.set_settings(settings)
 
-        if mdmc_input_override:
-            self.override_trajectory_input()
+        if trajectory_input == "mdmc":
+            self.mdmc_trajectory_input()
+        elif trajectory_input == "mock":
+            self.mock_trajectory_input()
 
-    def override_trajectory_input(self):
+    def mdmc_trajectory_input(self):
         """Remove the hdf_trajectory (file-based) from settings,
         and introduce an MDMC trajectory instead.
         """
         for key, value in self.settings.items():
             if key == "trajectory":
-                if value[0] == "hdf_trajectory":
-                    self.settings[key] = ("mdmc_trajectory", {})
+                if value[0] == "HDFTrajectoryConfigurator":
+                    self.settings[key] = ("MDMCTrajectoryConfigurator", {})
+
+    def mock_trajectory_input(self):
+        """Remove the hdf_trajectory (file-based) from settings,
+        and introduce a mock trajectory instead.
+        """
+        for key, value in self.settings.items():
+            if key == "trajectory":
+                if value[0] == "HDFTrajectoryConfigurator":
+                    self.settings[key] = ("MockTrajectoryConfigurator", {})
 
     def build_configuration(self):
         self._configuration.clear()

MDANSE/Src/Framework/Configurators/MDMCTrajectoryConfigurator.py → MDANSE/Src/MDANSE/Framework/Configurators/MDMCTrajectoryConfigurator.py

@@ -15,8 +15,6 @@
 
 import os
 
-from MDANSE import PLATFORM, REGISTRY
-
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 
@@ -86,6 +84,3 @@ def get_information(self):
             info.append("The trajectory does not contain atomic velocities\n")
 
         return "".join(info)
-
-
-REGISTRY["mdmc_trajectory"] = MDMCTrajectoryConfigurator

MDANSE/Src/MDANSE/Framework/Configurators/MockTrajectoryConfigurator.py

@@ -0,0 +1,87 @@
+# **************************************************************************
+#
+# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
+#
+# @file      Src/Framework/Configurators/MDMCTrajectoryConfigurator.py
+# @brief     A way to take in a trajectory from MDMC in a wrapper
+#
+# @homepage  https://www.isis.stfc.ac.uk/Pages/MDANSEproject.aspx
+# @license   GNU General Public License v3 or higher (see LICENSE)
+# @copyright Institut Laue Langevin 2013-now
+# @copyright ISIS Neutron and Muon Source, STFC, UKRI 2021-now
+# @authors   Scientific Computing Group at ILL (see AUTHORS)
+#
+# **************************************************************************
+
+import os
+
+from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
+from MDANSE.MolecularDynamics.MockTrajectory import MockTrajectory
+
+
+class MockTrajectoryConfigurator(IConfigurator):
+    """
+    This is a replacement for a trajectory stored in and HDF5 file.
+    It is intended to be a drop-in replacement for HDFTrajectoryConfigurator,
+    even though it is NOT file-based.
+    """
+
+    _default = None
+
+    def __init__(self, name, wildcard="JSON file|*.json", **kwargs):
+        """
+        Initializes the configurator object.
+
+        :param name: the name of the configurator as it will appear in the configuration.
+        :type name: str
+        :param wildcard: the wildcard used to filter the file. This will be used in MDANSE GUI when
+        browsing for the input file.
+        :type wildcard: str
+        """
+
+        # The base class constructor.
+        IConfigurator.__init__(self, name, **kwargs)
+
+        self._wildcard = wildcard
+
+    def configure(self, value: str):
+        """
+        Configure a mock trajectory file.
+
+        :param value: a JSON file with a MockTrajectory definition
+        :type value: str
+        """
+
+        self["value"] = value
+        self["filename"] = "Mock"
+
+        self["instance"] = MockTrajectory.from_json(value)
+
+        self["basename"] = "Mock"
+
+        self["length"] = len(self["instance"])
+
+        self["md_time_step"] = self["instance"]._time_step
+
+        self["has_velocities"] = self["instance"].has_velocities
+
+    def get_information(self):
+        """
+        Returns some basic informations about the contents of the HDF trajectory file.
+
+        :return: the informations about the contents of the HDF trajectory file.
+        :rtype: str
+        """
+
+        info = ["Mock trajectory used as input"]
+        info.append("Number of steps: %d\n" % self["length"])
+        info.append(
+            "Size of the chemical system: %d\n"
+            % self["instance"].chemical_system.number_of_atoms
+        )
+        if self["has_velocities"]:
+            info.append("The trajectory contains atomic velocities\n")
+        else:
+            info.append("The trajectory does not contain atomic velocities\n")
+
+        return "".join(info)

MDANSE/Src/MDANSE/Framework/Jobs/IJob.py

@@ -117,12 +117,12 @@ def define_unique_name():
 
         return name
 
-    def __init__(self, mdmc_input_override=False):
+    def __init__(self, trajectory_input="mdanse"):
         """
         The base class constructor.
         """
 
-        Configurable.__init__(self, mdmc_input_override=mdmc_input_override)
+        Configurable.__init__(self, trajectory_input=trajectory_input)
 
         self._outputData = OutputData()
 

MDANSE/Src/MDANSE/MolecularDynamics/MockTrajectory.py

@@ -155,7 +155,7 @@ def __getitem__(self, frame):
         configuration = {}
         configuration["coordinates"] = self.coordinates(frame).astype(np.float64)
         configuration["time"] = self._time_axis[frame]
-        configuration["unit_cell"] = self.unit_cell(frame).astype(np.float64)
+        configuration["unit_cell"] = self.unit_cell(frame)._unit_cell.astype(np.float64)
 
         return configuration
 
@@ -226,7 +226,7 @@ def unit_cell(self, frame):
         :rtype: ndarray
         """
 
-        return UnitCell(self._full_box_size)._unit_cell
+        return UnitCell(self._full_box_size)
 
     def __len__(self):
         """Returns the length of the trajectory.
@@ -451,6 +451,10 @@ def filename(self):
 
         return "nonexistent_file.h5"
 
+    @property
+    def has_velocities(self):
+        return "velocities" in self._variables.keys()
+
     def variables(self):
         """Return the configuration variables stored in this trajectory.
 

MDANSE/Tests/UnitTests/Analysis/test_mock_dynamics.py

@@ -24,14 +24,6 @@
 
 mock_json = os.path.join(file_wd, "..", "Data", "mock.json")
 
-@pytest.fixture(scope="module")
-def mock_trajectory():
-    """Returns a trajectory containing muiltiple atoms,
-    in a supercell, which move periodically.
-    """
-    traj = MockTrajectory.from_json(mock_json)
-    return traj
-
 
 @pytest.mark.parametrize(
     "interp_order, normalise",
@@ -44,16 +36,16 @@ def mock_trajectory():
         (3, False),
     ],
 )
-def test_vacf(mock_trajectory, interp_order, normalise):
+def test_vacf(interp_order, normalise):
     temp_name = tempfile.mktemp()
     parameters = {}
     parameters["frames"] = (0, 10, 1)
     parameters["interpolation_order"] = interp_order
     parameters["output_files"] = (temp_name, ("MDAFormat",))
     parameters["running_mode"] = ("monoprocessor",)
     parameters["normalize"] = normalise
-    parameters["trajectory"] = mock_trajectory
-    vacf = IJob.create("VelocityAutoCorrelationFunction")
+    parameters["trajectory"] = mock_json
+    vacf = IJob.create("VelocityAutoCorrelationFunction", trajectory_input="mock")
     vacf.run(parameters, status=True)
     assert path.exists(temp_name + ".mda")
     assert path.isfile(temp_name + ".mda")

MDANSE/Tests/UnitTests/test_mock_trajectory.py

@@ -58,6 +58,7 @@
 
 mock_json = os.path.join(file_wd, "Data", "mock.json")
 
+
 @pytest.fixture(scope="module")
 def static_trajectory():
     """Returns a trajectory containing a single atom,
@@ -70,6 +71,7 @@ def static_trajectory():
     traj.set_coordinates(np.array([[1.0, 0.0, 0.0]]))
     return traj
 
+
 @pytest.fixture
 def full_trajectory():
     """Returns a trajectory containing muiltiple atoms,
@@ -156,6 +158,7 @@ def test_modulation_multiple(full_trajectory):
     assert np.allclose(conf_init["coordinates"], conf_end["coordinates"])
     assert not np.allclose(conf_init["coordinates"], conf_between["coordinates"])
 
+
 def test_from_json(full_trajectory):
     full_trajectory.modulate_structure(
         np.array([[1.0, 1.0, 0.0], [0.0, 0.0, 1.0], [0.0, 0.0, 0.0]]),
@@ -172,7 +175,5 @@ def test_from_json(full_trajectory):
     instance = MockTrajectory.from_json(mock_json)
     assert full_trajectory._atom_types == instance._atom_types
     print(full_trajectory.coordinates(25) - instance.coordinates(25))
-    assert np.allclose(full_trajectory.coordinates(25),
-                       instance.coordinates(25))
-    assert not np.allclose(full_trajectory.coordinates(25),
-                       instance.coordinates(22))
+    assert np.allclose(full_trajectory.coordinates(25), instance.coordinates(25))
+    assert not np.allclose(full_trajectory.coordinates(25), instance.coordinates(22))