Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in…

…to minimum-effort-atom-labels

MDANSE/Extensions/fold_coordinates.pyx

@@ -76,22 +76,22 @@ def fold_coordinates(
             by = box_coords[i,j,1]
             bz = box_coords[i,j,2]
 
-            while bx < -0.5:
+            while bx < 0.0:
                 bx += 1.0
 
-            while by < -0.5:
+            while by < 0.0:
                 by += 1.0
 
-            while bz < -0.5:
+            while bz < 0.0:
                 bz += 1.0
 
-            while bx > 0.5:
+            while bx >= 1.0:
                 bx -= 1.0
 
-            while by > 0.5:
+            while by >= 1.0:
                 by -= 1.0
 
-            while bz > 0.5:
+            while bz >= 1.0:
                 bz -= 1.0
 
             box_coords[i,j,0] = bx

MDANSE/Src/MDANSE/Framework/Configurators/GroupingLevelConfigurator.py

@@ -110,17 +110,15 @@ def configure(self, value):
         trajConfig = self._configurable[self._dependencies["trajectory"]]
         atomSelectionConfig = self._configurable[self._dependencies["atom_selection"]]
 
-        allAtoms = sorted_atoms(trajConfig["chemical_system"].atom_list)
+        allAtoms = sorted_atoms(trajConfig["instance"].chemical_system.atom_list)
 
         groups = collections.OrderedDict()
         for i in range(atomSelectionConfig["selection_length"]):
             idx = atomSelectionConfig["indexes"][i][0]
             el = atomSelectionConfig["elements"][i][0]
             mass = atomSelectionConfig["masses"][i][0]
             at = allAtoms[idx]
-            lvl = LEVELS[value][
-                at.top_level_chemical_entity().__class__.__name__.lower()
-            ]
+            lvl = LEVELS[value][at.top_level_chemical_entity.__class__.__name__.lower()]
             parent = self.find_parent(at, lvl)
             d = groups.setdefault(parent, {})
             d.setdefault("indexes", []).append(idx)

MDANSE/Src/MDANSE/Framework/Converters/ASE.py

@@ -79,6 +79,10 @@ class ASE(Converter):
             "mini": 0,
         },
     )
+    settings["fold"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Fold coordinates into box"},
+    )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",
         {
@@ -156,6 +160,8 @@ def run_step(self, index):
             realConf = PeriodicRealConfiguration(
                 self._trajectory.chemical_system, coords, unitCell
             )
+            if self._configuration["fold"]["value"]:
+                realConf.fold_coordinates()
         else:
             realConf = RealConfiguration(
                 self._trajectory.chemical_system,

MDANSE/Src/MDANSE/Framework/Converters/CP2K.py

@@ -140,6 +140,10 @@ class CP2K(Converter):
             "dependencies": {"input_file": "pos_file"},
         },
     )
+    settings["fold"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Fold coordinates into box"},
+    )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",
         {
@@ -232,7 +236,8 @@ def run_step(self, index):
             self._trajectory.chemical_system, coords, unitcell, **variables
         )
 
-        realConf.fold_coordinates()
+        if self._configuration["fold"]["value"]:
+            realConf.fold_coordinates()
 
         self._trajectory.chemical_system.configuration = realConf
 

MDANSE/Src/MDANSE/Framework/Converters/DFTB.py

@@ -54,7 +54,7 @@ class DFTB(Forcite):
     )
     settings["fold"] = (
         "BooleanConfigurator",
-        {"default": True, "label": "Fold coordinates in to box"},
+        {"default": False, "label": "Fold coordinates into box"},
     )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",

MDANSE/Src/MDANSE/Framework/Converters/Discover.py

@@ -275,7 +275,7 @@ class Discover(Converter):
     )
     settings["fold"] = (
         "BooleanConfigurator",
-        {"default": True, "label": "Fold coordinates into box"},
+        {"default": False, "label": "Fold coordinates into box"},
     )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",

MDANSE/Src/MDANSE/Framework/Jobs/CroppedTrajectory.py

@@ -27,6 +27,8 @@ class CroppedTrajectory(IJob):
     Crop a trajectory in terms of the contents of the simulation box (selected atoms or molecules) and the trajectory length.
     """
 
+    enabled = False
+
     label = "Cropped Trajectory"
 
     category = (

MDANSE/Src/MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -49,6 +49,8 @@ class CurrentCorrelationFunction(IJob):
     in space and time)'
     """
 
+    enabled = False
+
     label = "Current Correlation Function"
 
     category = (

MDANSE/Src/MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py

@@ -25,6 +25,8 @@
 class DipoleAutoCorrelationFunction(IJob):
     """ """
 
+    enabled = False
+
     label = "Dipole AutoCorrelation Function"
 
     category = (

MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py

@@ -47,6 +47,8 @@ class GlobalMotionFilteredTrajectory(IJob):
     In the global motion filtered trajectory, the universe is made infinite and all the configurations contiguous.
     """
 
+    enabled = False
+
     label = "Global Motion Filtered Trajectory"
 
     category = (

MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py

@@ -56,6 +56,8 @@ class McStasVirtualInstrument(IJob):
         instrument resolution, self-shielding and multiple scattering.
     """
 
+    enabled = False
+
     label = "McStas Virtual Instrument"
 
     category = (

MDANSE/Src/MDANSE/Framework/Jobs/RadiusOfGyration.py

@@ -47,10 +47,6 @@ class RadiusOfGyration(IJob):
         "AtomSelectionConfigurator",
         {"dependencies": {"trajectory": "trajectory"}},
     )
-    settings["weights"] = (
-        "WeightsConfigurator",
-        {"dependencies": {"atom_selection": "atom_selection"}},
-    )
     settings["output_files"] = (
         "OutputFilesConfigurator",
         {"formats": ["MDAFormat", "TextFormat"]},

MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py

@@ -46,6 +46,8 @@ class RigidBodyTrajectory(IJob):
     doi: 10.1080/08927029108022453.
     """
 
+    enabled = False
+
     label = "Rigid Body Trajectory"
 
     category = (

MDANSE/Tests/UnitTests/Analysis/test_scattering.py

@@ -32,7 +32,7 @@ def qvector_spherical_lattice(trajectory):
     )
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(scope="module")
 def dcsf():
     temp_name = tempfile.mktemp()
     parameters = {}
@@ -45,7 +45,7 @@ def dcsf():
         "SphericalLatticeQVectors",
         {"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
     )
-    parameters["running_mode"] = ("monoprocessor",)
+    parameters["running_mode"] = ("single-core",)
     parameters["trajectory"] = short_traj
     parameters["weights"] = "b_coherent"
     dcsf = IJob.create("DynamicCoherentStructureFactor")
@@ -54,7 +54,7 @@ def dcsf():
     os.remove(temp_name + ".mda")
 
 
-@pytest.fixture(scope="function")
+@pytest.fixture(scope="module")
 def disf():
     temp_name = tempfile.mktemp()
     parameters = {}
@@ -67,7 +67,7 @@ def disf():
         "SphericalLatticeQVectors",
         {"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
     )
-    parameters["running_mode"] = ("monoprocessor",)
+    parameters["running_mode"] = ("single-core",)
     parameters["trajectory"] = short_traj
     parameters["weights"] = "b_incoherent2"
     disf = IJob.create("DynamicIncoherentStructureFactor")
@@ -151,35 +151,29 @@ def test_gdisf(trajectory):
     os.remove(temp_name + ".mda")
 
 
-@pytest.mark.xfail(reason="see docstring")
 def test_ndtsf(disf, dcsf, qvector_spherical_lattice):
-    """A known problem that will have to be fixed."""
     temp_name = tempfile.mktemp()
     parameters = {}
     parameters["atom_selection"] = None
     parameters["atom_transmutation"] = None
-    parameters["frames"] = (0, 10, 1)
     parameters["disf_input_file"] = disf
     parameters["dcsf_input_file"] = dcsf
-    parameters["q_vectors"] = qvector_spherical_lattice
-    parameters["running_mode"] = ("monoprocessor",)
+    parameters["running_mode"] = ("single-core",)
     parameters["trajectory"] = short_traj
     parameters["output_files"] = (temp_name, ("MDAFormat",))
-    parameters["weights"] = "b_incoherent2"
     ndtsf = IJob.create("NeutronDynamicTotalStructureFactor")
     ndtsf.run(parameters, status=True)
     assert path.exists(temp_name + ".mda")
     assert path.isfile(temp_name + ".mda")
     os.remove(temp_name + ".mda")
 
 
-@pytest.mark.xfail(reason="see docstring")
 def test_ssfsf(disf):
     """Also fails at the moment. Must be fixed soon"""
     temp_name = tempfile.mktemp()
     parameters = {}
     parameters["sample_inc"] = disf
-    parameters["running_mode"] = ("monoprocessor",)
+    parameters["running_mode"] = ("single-core",)
     parameters["instrument_resolution"] = ("Ideal", {})
     parameters["output_files"] = (temp_name, ("MDAFormat",))
     ndtsf = IJob.create("StructureFactorFromScatteringFunction")
@@ -203,7 +197,7 @@ def test_ccf(qvector_spherical_lattice):
     parameters["interpolation_mode"] = "automatic"
     parameters["output_files"] = (temp_name, ("MDAFormat",))
     parameters["q_vectors"] = qvector_spherical_lattice
-    parameters["running_mode"] = ("monoprocessor",)
+    parameters["running_mode"] = ("single-core",)
     parameters["trajectory"] = short_traj
     parameters["weights"] = "b_coherent"
     ndtsf = IJob.create("CurrentCorrelationFunction")

MDANSE/Tests/UnitTests/test_configuration.py

@@ -449,9 +449,9 @@ def test_fold_coordinates(self):
             np.allclose(
                 conf["coordinates"],
                 [
-                    [-0.65955991, 1.40648987, -1.9977125],
-                    [1.04665145, -1.06488218, -0.1532281],
-                    [-0.27479577, -0.08878546, 1.93534948],
+                    [1.34044009, 2.40648987, -1.9977125],
+                    [0.04665145, 1.93511782, -0.1532281],
+                    [1.72520423, 0.91121454, -2.06465052],
                     [-0.22366532, 1.38389029, -0.29560999],
                 ],
                 rtol=1.0e-6,