Fix parsing logic for CREST runs

isicle/parse.py

@@ -922,41 +922,40 @@ def _crest_timing(self):
         """
 
         def grab_time(line):
-            line = line.replace(" ", "")
-            line = line.split(":")
-
-            return ":".join(line[1:]).strip("\n")
+            # Regular expression pattern
+            pattern = r"(?:(\d+)\s*d,\s*)?(?:(\d+)\s*h,\s*)?(?:(\d+)\s*min,\s*)?([\d.]+)\s*sec"
+            match = re.search(pattern, line)
+            return {
+                "days": int(match.group(1)) if match.group(1) else 0,
+                "hours": int(match.group(2)) if match.group(2) else 0,
+                "minutes": int(match.group(3)) if match.group(3) else 0,
+                "seconds": float(match.group(4))
+                }
 
-        ready = False
+        timing = {}
         for line in self.lines:
-            if "test MD wall time" in line:
-                test_MD = grab_time(line)
-                ready = True
+            if "CREST runtime (total)" in line:
+                timing["CREST runtime (total)"] = grab_time(line)
 
-            if "MTD wall time" in line:
-                MTD_time = grab_time(line)
+            if "Trial metadynamics (MTD)" in line:
+                timing["Trial metadynamics (MTD)"] = grab_time(line)
 
-            if "multilevel OPT wall time" in line:
-                multilevel_OPT = grab_time(line)
+            if "Metadynamics (MTD)" in line:
+                timing["Metadynamics (MTD)"] = grab_time(line)
 
-            if "MD wall time" in line and ready is True:
-                MD = grab_time(line)
-                ready = False
+            if "Geometry optimization" in line:
+                timing["Geometry optimization"] = grab_time(line)
 
-            if "GC wall time" in line:
-                GC = grab_time(line)
+            if "Molecular dynamics (MD)" in line:
+                timing["Molecular dynamics (MD)"] = grab_time(line)
 
-            if "Overall wall time" in line:
-                overall = grab_time(line)
+            if "Genetic crossing (GC)" in line:
+                timing["Genetic crossing (GC)"] = grab_time(line)
+
+            if "I/O and setup" in line:
+                timing["I/O and setup"] = grab_time(line)
 
-        return {
-            "test MD wall time": test_MD,
-            "metadynamics wall time": MTD_time,
-            "multilevel opt wall time": multilevel_OPT,
-            "molecular dynamics wall time": MD,
-            "genetic z-matrix crossing wall time": GC,
-            "overall wall time": overall,
-        }
+        return timing
 
     def _isomer_energy(self):
         """
@@ -1060,10 +1059,12 @@ def _parse_protocol(self):
         protocol = None
 
         for line in self.lines:
-            if " > " in line:
+            if "$ crest" in line:
                 protocol = line.strip("\n")
+                return protocol
             if "program call" in line:
                 protocol = (line.split(":")[1]).strip("\n")
+                return protocol
         return protocol
 
     def _parse_geometry(self):
@@ -1100,15 +1101,15 @@ def parse(self):
 
         # Check that the file is valid first
         if len(self.lines) == 0:
-            raise RuntimeError("No contents to parse: {}".format(self.path))
+            raise RuntimeError("No contents to parse.")
 
         last_lines = "".join(self.lines[-10:])
         if (
             ("terminat" not in last_lines)
             & ("normal" not in last_lines)
             & ("ratio" not in last_lines)
         ):
-            raise RuntimeError("XTB job failed: {}".format(self.path))
+            raise RuntimeError("XTB job failed.")
 
         # Initialize result object to store info
         result = {