Merge pull request #286 from TheoChem-VU/276-exception-raised-while-t…

…rying-to-read-charge-from-orca-calculations

Fixed an issue where reading ORCA calculations would crash the program

src/tcutility/results/__init__.py

@@ -105,16 +105,13 @@ def read(calc_dir: Union[str, pl.Path]) -> Result:
     elif ret.engine == "orca":
         try:
             ret.orca = orca.get_calc_settings(ret)
-        except:
+        except:  # noqa
             ret.orca = None
-            print('Error reading:', calc_dir)
-            raise
+
         try:
             ret.properties = orca.get_properties(ret)
-        except:
+        except:  # noqa
             ret.properties = None
-            print('Error reading:', calc_dir)
-            raise
 
     # unload cached KFReaders associated with this calc_dir
     to_delete = [key for key in cache._cache if key.startswith(os.path.abspath(calc_dir))]

src/tcutility/results/orca.py

@@ -9,7 +9,7 @@
 
 
 def get_calc_files(calc_dir: str) -> Result:
-    """Function that returns files relevant to AMS calculations stored in ``calc_dir``.
+    """Function that returns files relevant to ORCA calculations stored in ``calc_dir``.
 
     Args:
         calc_dir: path pointing to the desired calculation
@@ -22,18 +22,22 @@ def get_calc_files(calc_dir: str) -> Result:
     for root, _, files_ in os.walk(calc_dir):
         files.extend([j(root, file) for file in files_])
 
-    # parse the filenames
+    # we now go through all the files and check their nature
     ret = Result()
     ret.root = os.path.abspath(calc_dir)
     for file in files:
-        try:
-            with open(file) as f:
-                lines = f.readlines()
-
+        with open(file, errors='ignore') as f:
+            lines = f.readlines()
+            # detect the output file
             if any(["* O   R   C   A *" in line for line in lines]):
                 ret.out = os.path.abspath(file)
-        except:  # noqa
-            pass
+                continue    
+
+            # detect the input file
+            # there should be lines starting with ! and also the system line, starting with * xyz, * xyzfile, * gzmtfile or * int
+            if any([line.startswith('!') for line in lines]) and any([(len(line.split()) > 2 and line.split()[0] == '*' and line.split()[1] in ['xyz', 'xyzfile', 'gzmtfile', 'int']) for line in lines]):
+                ret.inp = os.path.abspath(file)
+                continue
 
     return ret
 
@@ -81,22 +85,29 @@ def get_input(info: Result) -> Result:
             - **task (str)** - the task that was performed by the calculation, e.g. "SinglePoint", "TransitionStateSearch".
     """
     ret = Result()
-    with open(info.files.out) as out:
-        start_reading = False
-        lines = []
-        for line in out.readlines():
-            line = line.strip()
-            if start_reading:
-                lines.append(line)
 
-            if "INPUT FILE" in line:
-                start_reading = True
-                continue
+    # we read the input file first
+    if 'inp' in info.files:
+        with open(info.files.inp) as inp:
+            lines = inp.readlines()
+    # if we don't have it we read the output file, which contains the input as a block
+    else:
+        with open(info.files.out) as out:
+            start_reading = False
+            lines = []
+            for line in out.readlines():
+                line = line.strip()
+                if start_reading:
+                    lines.append(line)
 
-            if "****END OF INPUT****" in line:
-                break
+                if "INPUT FILE" in line:
+                    start_reading = True
+                    continue
+
+                if "****END OF INPUT****" in line:
+                    break
 
-    lines = [line.split(">")[1] for line in lines[2:-1] if line.split(">")[1].strip()]
+        lines = [line.split(">")[1] for line in lines[2:-1] if line.split(">")[1].strip()]
 
     ret.main = []
     curr_section = None