added fake _xdr attributes in case the trajectory was constructed by other means than reading a gromacs xtc file

src/mdevaluate/checksum.py

@@ -102,8 +102,20 @@ def checksum(*args, csum=None, _seen=None):
         _seen.add(obj_id)
 
         if hasattr(arg, "__checksum__"):
-            logger.debug("Checksum via __checksum__: %s", str(arg))
-            csum.update(str(arg.__checksum__()).encode())
+            method = getattr(arg, "__checksum__")
+            if callable(method) and not isinstance(arg, type):
+                logger.debug("Checksum via __checksum__: %s", str(arg))
+                csum.update(str(method()).encode())
+            elif isinstance(arg, type):
+                try:
+                    src = inspect.getsource(arg)
+                    csum.update(strip_comments(src).encode())
+                    logger.debug("Checksum via class source for %s", arg.__name__)
+                except (OSError, TypeError):
+                    csum.update(arg.__name__.encode())
+                    logger.debug("Checksum via class name for %s", arg.__name__)
+            else:
+                logger.debug("Skipping unbound __checksum__ on %s", type(arg))
         elif isinstance(arg, bytes):
             csum.update(arg)
         elif isinstance(arg, str):

src/mdevaluate/coordinates.py

@@ -413,7 +413,6 @@ def center_of_masses(
 ) -> NDArray:
     if atom_indices is None:
         atom_indices = list(range(len(frame)))
-    print(type(frame))
     res_ids = frame.residue_ids[atom_indices]
     masses = frame.masses[atom_indices]
     if shear:

src/mdevaluate/correlation.py

@@ -147,7 +147,8 @@ def shifted_correlation(
     num_frames = int(len(frames) * window)
     ls = np.logspace(0, np.log10(num_frames + 1), num=points)
     idx = np.unique(np.int_(ls) - 1)
-    t = np.array([frames[i].time for i in idx]) - frames[0].time
+    dt = round(frames[1].time - frames[0].time, 6) # round to avoid bad floats
+    t = idx * dt
 
     result = np.array(
         [

src/mdevaluate/reader.py

@@ -23,6 +23,8 @@ from .logging_util import logger
 from . import atoms
 from .coordinates import Coordinates
 
+from unittest.mock import MagicMock
+
 CSR_ATTRS = ("data", "indices", "indptr")
 NOJUMP_MAGIC = 2016
 Group_RE = re.compile(r"\[ ([-+\w]+) \]")
@@ -240,7 +242,18 @@ def generate_nojump_matrices(trajectory: Coordinates):
     save_nojump_matrices(trajectory.frames)
 
 
+def _ensure_xdr(reader: BaseReader):
+    """Patch missing _xdr attribute for non-XDR readers (e.g. LAMMPS DumpReader)
+    with a stable mock so checksums are consistent across runs."""
+    if not hasattr(reader.rd, '_xdr'):
+        mock_xdr = MagicMock()
+        mock_xdr.offsets = np.arange(len(reader))
+        print(f"Adding mock _xdr attribute for to reader of length {len(reader)}.")
+        reader.rd._xdr = mock_xdr
+
+
 def save_nojump_matrices(reader: BaseReader, matrices: npt.ArrayLike = None):
+    _ensure_xdr(reader)
     if matrices is None:
         matrices = reader.nojump_matrices
     data = {"checksum": checksum(NOJUMP_MAGIC, checksum(reader))}
@@ -253,6 +266,7 @@ def save_nojump_matrices(reader: BaseReader, matrices: npt.ArrayLike = None):
 
 
 def load_nojump_matrices(reader: BaseReader):
+    _ensure_xdr(reader)
     zipname = nojump_load_filename(reader)
     try:
         data = np.load(zipname, allow_pickle=True)

src/mdevaluate/utils.py

@@ -334,6 +334,11 @@ def quick1etau(t: ArrayLike, C: ArrayLike, n: int = 7) -> float:
     C is C(t) the correlation function
     n is the minimum number of points around 1/e required
     """
+    # norm, if t=0 provided
+    if t[0] == 0:
+        C /= C[0]
+    C, t = C[t>0], t[t>0] # make sure t=0 is dropped
+
     # first rough estimate, the closest time. This is returned if the interpolation fails!
     tau_est = t[np.argmin(np.fabs(C - np.exp(-1)))]
     # reduce the data to points around 1/e