Connect the new parameters to TrajectoryWriter

ISISNeutronMuon · Jan 29, 2024 · c86794c · c86794c
1 parent bbd7fa4
commit c86794c
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Showing 17 changed files with 40 additions and 8 deletions.
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/ASE.py b/MDANSE/Src/MDANSE/Framework/Converters/ASE.py
@@ -106,6 +106,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._nameToIndex = dict(
@@ -328,6 +330,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._nameToIndex = dict(

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/CASTEP.py b/MDANSE/Src/MDANSE/Framework/Converters/CASTEP.py
@@ -246,6 +246,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemical_system,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py b/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py
@@ -299,8 +299,9 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemical_system,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
-        # A MMTK trajectory is opened for writing.
 
         data_to_be_written = ["configuration", "time"]
         if self.configuration["vel_file"]:

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/DCD.py b/MDANSE/Src/MDANSE/Framework/Converters/DCD.py
@@ -333,6 +333,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemical_system,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py b/MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py
@@ -424,6 +424,8 @@ def initialize(self):
             self.configuration["output_files"]["files"][0],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._velocities = None

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Discover.py b/MDANSE/Src/MDANSE/Framework/Converters/Discover.py
@@ -326,6 +326,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py b/MDANSE/Src/MDANSE/Framework/Converters/Forcite.py
@@ -341,6 +341,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py b/MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py
@@ -127,7 +127,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             chemical_system,
             self.numberOfSteps,
-            positions_dtype=np.float32,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py b/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py
@@ -234,6 +234,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._nameToIndex = dict(

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/VASP.py b/MDANSE/Src/MDANSE/Framework/Converters/VASP.py
@@ -222,6 +222,8 @@ def initialize(self):
             self.configuration["output_file"]["file"],
             self._chemicalSystem,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/CenterOfMassesTrajectory.py
@@ -88,6 +88,8 @@ def initialize(self):
             self.configuration["output_file"]["files"][0],
             chemical_system,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._grouped_atoms = group_atoms(

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/CroppedTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/CroppedTrajectory.py
@@ -76,6 +76,8 @@ def initialize(self):
             self.configuration["trajectory"]["instance"].chemical_system,
             self.numberOfSteps,
             self._selectedAtoms,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/GlobalMotionFilteredTrajectory.py
@@ -103,6 +103,8 @@ def initialize(self):
             self.configuration["trajectory"]["instance"].chemical_system,
             self.numberOfSteps,
             self._selected_atoms.atom_list,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         # This will store the configuration used as the reference for the following step.

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/MoleculeFinder.py b/MDANSE/Src/MDANSE/Framework/Jobs/MoleculeFinder.py
@@ -80,6 +80,8 @@ def initialize(self):
             self.configuration["output_files"]["files"][0],
             chemical_system,
             self.numberOfSteps,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py
@@ -139,6 +139,8 @@ def initialize(self):
             trajectory.chemical_system,
             self.configuration["frames"]["number"],
             selectedAtoms,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
         self._group_atoms = [group.atom_list for group in self._groups]

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/UnfoldedTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/UnfoldedTrajectory.py
@@ -76,6 +76,8 @@ def initialize(self):
             self.configuration["trajectory"]["instance"].chemical_system,
             self.numberOfSteps,
             self._selectedAtoms,
+            positions_dtype=self.configuration["output_file"]["dtype"],
+            compression=self.configuration["output_file"]["compression"],
         )
 
     def run_step(self, index):

diff --git a/MDANSE/Tests/UnitTests/test_converter.py b/MDANSE/Tests/UnitTests/test_converter.py
@@ -28,7 +28,7 @@ def test_lammps_mdt_conversion_file_exists_and_loads_up_successfully():
     parameters["config_file"] = lammps_config
     parameters["mass_tolerance"] = 0.05
     parameters["n_steps"] = 0
-    parameters["output_file"] = (temp_name, "MDTFormat")
+    parameters["output_file"] = (temp_name, 64, 'lza')
     parameters["smart_mass_association"] = True
     parameters["time_step"] = 1.0
     parameters["trajectory_file"] = lammps_lammps
@@ -65,7 +65,7 @@ def test_vasp_mdt_conversion_file_exists_and_loads_up_successfully():
 
     parameters = {
         "fold": False,
-        "output_file": (temp_name, "MDTFormat"),
+        "output_file": (temp_name, 64, 'lza'),
         "time_step": 1.0,
         "xdatcar_file": vasp_xdatcar,
     }
@@ -85,7 +85,7 @@ def test_discover_mdt_conversion_file_exists_and_loads_up_successfully():
     parameters = {
         "fold": True,
         "his_file": discover_his,
-        "output_file": (temp_name, "MDTFormat"),
+        "output_file": (temp_name, 64, 'lza'),
         "xtd_file": discover_xtd,
     }
 
@@ -105,7 +105,7 @@ def test_charmm_mdt_conversion_file_exists_and_loads_up_successfully():
     parameters = {
         "dcd_file": hem_cam_dcd,
         "fold": False,
-        "output_file": (temp_name, "MDTFormat"),
+        "output_file": (temp_name, 64, 'lza'),
         "pdb_file": hem_cam_pdb,
         "time_step": 1.0,
     }
@@ -126,7 +126,7 @@ def test_ase_mdt_conversion_file_exists_and_loads_up_successfully():
     parameters = {
         "trajectory_file": ase_traj,
         "fold": False,
-        "output_file": (temp_name, "MDTFormat"),
+        "output_file": (temp_name, 64, 'lza'),
         "n_steps": 0,
         "time_step": 50.0,
         "time_unit": "fs",
@@ -142,7 +142,7 @@ def test_xyz_mdt_conversion_file_exists_and_loads_up_successfully():
     parameters = {
         "trajectory_file": xyz_traj,
         "fold": False,
-        "output_file": (temp_name, "MDTFormat"),
+        "output_file": (temp_name, 64, 'lza'),
         "n_steps": 0,
         "time_step": 50.0,
         "time_unit": "fs",