fix thermo_lines not being reset

pyiron_atomistics/lammps/output.py

@@ -325,27 +325,25 @@ def _collect_output_log(
     with open(file_name, "r") as f:
         dfs = []
         read_thermo = False
-        thermo_lines = ""
         for l in f:
             l = l.lstrip()
 
+            if l.startswith("Step"):
+                thermo_lines = ""
+                read_thermo = True
+
             if read_thermo:
                 if l.startswith("Loop") or l.startswith("ERROR"):
                     read_thermo = False
                     dfs.append(
                         pd.read_csv(StringIO(thermo_lines), sep="\s+", engine="c")
                     )
-                    continue
 
                 elif l.startswith("WARNING:"):
                     logger.warning(f"A warning was found in the log:\n{l}")
-                    continue
 
-                thermo_lines += l
-
-            if l.startswith("Step"):
-                read_thermo = True
-                thermo_lines += l
+                else:
+                    thermo_lines += l
 
     h5_dict = {
         "Step": "steps",
@@ -361,7 +359,7 @@ def _collect_output_log(
         for i in range(len(dfs)):
             df = dfs[i]
             df["LogStep"] = np.ones(len(df)) * i
-        df = pd.concat(dfs)
+        df = pd.concat(dfs, ignore_index=True)
 
     for key in df.columns[df.columns.str.startswith("f_mean")]:
         h5_dict[key] = key.replace("f_", "")