fix cosmo directory and parse bug

Author: gmiralles7

isicle/parse.py

@@ -398,7 +398,7 @@ def _parse_shielding(self):
         shield_idxs = []
         shield_atoms = []
         shields = []
-
+        collect_idx = False # changed
         for line in self.data["out"].split("\n"):
             if " SHIELDING" in line:
                 shield_idxs = [int(x) for x in line.split()[2:]]

isicle/qm.py

@@ -906,9 +906,12 @@ def finish(self):
         cosmo = False
         geomfiles = sorted([x for x in outfiles if x.endswith(".xyz")])
         outfiles = sorted([x for x in outfiles if not x.endswith(".xyz")])
-        if "cosmo.xyz" in geomfiles:
-            geomfiles = [i for i in geomfiles if i != "cosmo.xyz"]
+
+        print('FILES', geomfiles) #changed cosmo.xyz
+        if os.path.join(self.temp_dir, "cosmo.xyz") in geomfiles: #changed cosmo.xyz
+            geomfiles = [i for i in geomfiles if i != os.path.join(self.temp_dir, "cosmo.xyz")]
             cosmo = True
+        print("COSMO", cosmo) #changed cosmo.xyz
 
         # Enumerate geometry files
         result["xyz"] = OrderedDict()
@@ -927,7 +930,7 @@ def finish(self):
 
         # Parse cosmo.xyz
         if cosmo is True:
-            with open("cosmo.xyz", "r") as f:
+            with open(os.path.join(self.temp_dir, "cosmo.xyz"), "r") as f: #changed cosmo.xyz
                 contents = f.read()
             result["cosmo"] = contents