added dcd, discover and vasp converter unit tests and bug fixes

ISISNeutronMuon · Jan 22, 2024 · e79f176 · e79f176
1 parent 211370b
commit e79f176
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Showing 10 changed files with 35,776 additions and 18 deletions.
diff --git a/MDANSE/MANIFEST.in b/MDANSE/MANIFEST.in
@@ -5,7 +5,7 @@ recursive-include Extensions/qhull_lib *.h *c *.pxd
 recursive-include Extensions/xtc *.h *c *.pxd
 recursive-include Src/MDANSE/Chemistry *.json
 recursive-include Src/MDANSE/Framework *.json
-recursive-include Tests *.pdb *.mdt *.config *.lammps
+recursive-include Tests/Data/*
 
 recursive-include Doc *
 

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/DCD.py b/MDANSE/Src/MDANSE/Framework/Converters/DCD.py
@@ -156,7 +156,7 @@ def read_header(self):
         # Read a block
         data = self.next_record()
 
-        if data[:4] != "CORD":
+        if data[:4] != b"CORD":
             raise DCDFileError("Unrecognized DCD format")
 
         temp = struct.unpack(self.byteOrder + "20i", data[4:])
@@ -198,22 +198,22 @@ def read_header(self):
         # Read a block
         data = self.next_record()
 
-        nLines = struct.unpack(self.byteOrder + b"I", data[0:4])[0]
+        nLines = struct.unpack(self.byteOrder.encode() + b"I", data[0:4])[0]
 
         self["title"] = []
         for i in range(nLines):
             temp = struct.unpack(
                 self.byteOrder + "80c", data[4 + 80 * i : 4 + 80 * (i + 1)]
             )
-            self["title"].append("".join(temp).strip())
+            self["title"].append(b"".join(temp).strip())
 
-        self["title"] = "\n".join(self["title"])
+        self["title"] = b"\n".join(self["title"])
 
         # Read a block
         data = self.next_record()
 
         # Read the number of atoms.
-        self["natoms"] = struct.unpack(self.byteOrder + b"I", data)[0]
+        self["natoms"] = struct.unpack(self.byteOrder.encode() + b"I", data)[0]
 
     def read_step(self):
         """

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Discover.py b/MDANSE/Src/MDANSE/Framework/Converters/Discover.py
@@ -341,7 +341,7 @@ def run_step(self, index):
 
         conf = self._trajectory.chemical_system.configuration
         if conf.is_periodic:
-            conf.unit_cell = cell
+            conf.unit_cell = UnitCell(cell)
 
         movableAtoms = self._hisfile["movable_atoms"]
 

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/VASP.py b/MDANSE/Src/MDANSE/Framework/Converters/VASP.py
@@ -45,10 +45,10 @@ def __init__(self, filename):
         while True:
             self._headerSize = self["instance"].tell()
             line = self["instance"].readline().strip()
-            if not line or line.lower().startswith("direct"):
+            if not line or line.lower().startswith(b"direct"):
                 self._frameHeaderSize = self["instance"].tell() - self._headerSize
                 break
-            header.append(line)
+            header.append(line.decode())
 
         self["scale_factor"] = float(header[0])
 
@@ -74,7 +74,7 @@ def __init__(self, filename):
         while True:
             self._frameSize = self["instance"].tell()
             line = self["instance"].readline().strip()
-            if not line or line.lower().startswith("direct"):
+            if not line or line.lower().startswith(b"direct"):
                 break
             nAtoms += 1
 
@@ -207,7 +207,7 @@ def initialize(self):
         self._xdatcarFile = XDATCARFile(self.configuration["xdatcar_file"]["filename"])
 
         # The number of steps of the analysis.
-        self.numberOfSteps = self._xdatcarFile["n_frames"]
+        self.numberOfSteps = int(self._xdatcarFile["n_frames"])
 
         self._chemicalSystem = ChemicalSystem()