Fix plot x axis

src/gemdat/plots/matplotlib/_msd_per_element.py

@@ -36,7 +36,7 @@ def msd_per_element(
     fig, ax = plt.subplots()
 
     # Since we want to plot in picosecond, we convert the time units
-    time_ps = trajectory.time_step * 1e12
+    time_ps = trajectory.time_step / 1000
     t_values = np.arange(len(trajectory)) * time_ps
 
     for sp in species:

src/gemdat/plots/plotly/_msd_per_element.py

@@ -27,7 +27,7 @@ def msd_per_element(*, trajectory: Trajectory) -> go.Figure:
     species = list(set(trajectory.species))
 
     # Since we want to plot in picosecond, we convert the time units
-    time_ps = trajectory.time_step * 1e12
+    time_ps = trajectory.time_step / 1000
 
     for sp in species:
         traj = trajectory.filter(sp.symbol)

src/gemdat/trajectory.py

@@ -6,6 +6,7 @@
 import hashlib
 import json
 import pickle
+import re
 import xml.etree.ElementTree as ET
 from itertools import compress, pairwise
 from pathlib import Path
@@ -26,6 +27,9 @@
     from .volume import Volume
 
 
+SP_NAME = re.compile(r'([a-zA-Z]+)')
+
+
 def _lengths(vectors: np.ndarray, lattice: Lattice) -> np.ndarray:
     """Calculate vector lengths using the metric tensor (Dunitz 1078, p227).
 
@@ -371,7 +375,6 @@ def from_gromacs(
         cache : Optional[Path], optional
             Path to cache data for vasprun.xml
 
-
         Returns
         -------
         trajectory : Trajectory
@@ -383,7 +386,6 @@ def from_gromacs(
 
         topology_file = str(topology_file)
         coords_file = str(coords_file)
-        edr_file = str(edr_file)
 
         if not cache:
             kwargs = {
@@ -414,7 +416,7 @@ def from_gromacs(
             lattice = Lattice.from_parameters(*utraj.trajectory[0].dimensions)
             coords = lattice.get_fractional_coords(coords)
 
-        species = [Element(sp.capitalize()) for sp in utraj.atoms.names]
+        species = [Element(SP_NAME.match(sp).group().capitalize()) for sp in utraj.atoms.names]  # type: ignore
 
         site_properties = {
             'residue': [sp.residue for sp in utraj.atoms],
@@ -427,14 +429,15 @@ def from_gromacs(
         }
 
         if edr_file:
+            edr_file = str(edr_file)
             aux = mda.auxiliary.EDR.EDRReader(edr_file)
             metadata['aux'] = aux.get_data(aux.terms)
 
         obj = cls(
             species=species,
             coords=coords,
             lattice=lattice,
-            time_step=utraj.trajectory.dt * 1000,
+            time_step=utraj.trajectory.dt * 1000,  # ps -> fs
             constant_lattice=constant_lattice,
             metadata=metadata,
             site_properties=site_properties,