Bug fixes for f-string handling and references to opt_level in config

config.py

@@ -324,11 +324,15 @@ def find_obabel():
             solvent_selected = None
         else:
             solvent_selected = avo_input["solvent"]
+
         # Update solvent
         config["solvent"] = solvent_selected
 
         # Update method
         config["method"] = methods.index(avo_input["method"])
 
+        # Update optimization level
+        config["opt_lvl"] = avo_input["opt_lvl"]
+
         with open(config_file, "w", encoding="utf-8") as config_path:
             json.dump(config, config_path, indent=2)

energy.py

@@ -90,7 +90,7 @@ def energy(
         result = {"moleculeFormat": "cjson", "cjson": avo_input["cjson"]}
         # Currently Avogadro ignores the energy result
         result["message"] = (
-            f"Energy from GFN{config["method"]}-xTB:\n"
+            f"Energy from GFN{config['method']}-xTB:\n"
             + f"{str(round(energy_hartree, 7))} hartree\n"
             + f"{str(round(energies['eV'], 7))} eV\n"
             + f"{str(round(energies['kJ'], 7))} kJ/mol\n"

freq.py

@@ -107,9 +107,9 @@ def frequencies(
         if float(freq_cjson["vibrations"]["frequencies"][0]) < 0:
             result["message"] = (
                 "At least one negative frequency found!\n"
-                "This is not a minimum on the potential energy surface.\n"
-                "You should reoptimize the geometry.\n"
-                "This can be avoided in future by using the Opt + Freq method."
+                + "This is not a minimum on the potential energy surface.\n"
+                + "You should reoptimize the geometry.\n"
+                + "This can be avoided in future by using the Opt + Freq method."
             )
 
         # Save result

md.py

@@ -121,7 +121,7 @@ def md(
                 "save_dir": {
                     "type": "string",
                     "label": "Save results in",
-                    "default": "<plugin_directory>/last",
+                    "default": str(calc_dir),
                 },
             },
         }
@@ -205,7 +205,10 @@ def md(
                     ].extend(xyz)
 
         # If user specified a save location, copy calculation directory to there
-        if avo_input["save_dir"] != "<plugin_directory>/last":
+        if not (
+            avo_input["save_dir"] in ["", None]
+            or Path(avo_input["save_dir"]) == calc_dir
+        ):
             copytree(calc_dir, Path(avo_input["save_dir"]), dirs_exist_ok=True)
 
         # Save result

ohess.py

@@ -98,7 +98,7 @@ def opt_freq(
             multiplicity=avo_input["spin"],
             solvation=config["solvent"],
             method=config["method"],
-            level=config["level"],
+            level=config["opt_lvl"],
         )
 
         # Convert frequencies
@@ -141,8 +141,8 @@ def opt_freq(
         if float(freq_cjson["vibrations"]["frequencies"][0]) < 0:
             result["message"] = (
                 "At least one negative frequency found!\n"
-                "This is not a minimum on the potential energy surface.\n"
-                "You should reoptimize the geometry."
+                + "This is not a minimum on the potential energy surface.\n"
+                + "You should reoptimize the geometry."
             )
 
         # Save result

opt.py

@@ -87,7 +87,7 @@ def optimize(
             multiplicity=avo_input["spin"],
             solvation=config["solvent"],
             method=config["method"],
-            level=config["level"],
+            level=config["opt_lvl"],
         )
 
         # Read the xyz file

run_calc.py

@@ -55,7 +55,7 @@
                 "command": {
                     "type": "string",
                     "label": "Command to run",
-                    "default": f"xtb <geometry_file> --opt {config["level"]} --chrg 0 --uhf 0",
+                    "default": f"xtb <geometry_file> --opt {config['opt_lvl']} --chrg 0 --uhf 0",
                     "order": 10.0,
                 },
                 "help": {
@@ -182,16 +182,16 @@
                 if distorted_geom.exists():
                     message.append(
                         "At least one negative frequency found!\n"
-                        "This is not a minimum on the potential energy surface.\n"
-                        "You should reoptimize the geometry starting from the\n"
-                        "distorted geometry found in the calculation directory\n"
-                        "with the filename 'xtbhess.xyz' or 'xtbhess.tmol'."
+                        + "This is not a minimum on the potential energy surface.\n"
+                        + "You should reoptimize the geometry starting from the\n"
+                        + "distorted geometry found in the calculation directory\n"
+                        + "with the filename 'xtbhess.xyz' or 'xtbhess.tmol'."
                     )
                 else:
                     message.append(
                         "At least one negative frequency found!\n"
-                        "This is not a minimum on the potential energy surface.\n"
-                        "You should reoptimize the geometry."
+                        + "This is not a minimum on the potential energy surface.\n"
+                        + "You should reoptimize the geometry."
                     )
 
         # Check if orbitals were requested