Fixed confirmed specifications for Gaussian

ccinput/packages/gaussian.py

@@ -368,14 +368,35 @@ def create_input_file(self):
             else:
                 cmd_formatted = f"{cmd} "
 
+            if cmd.lower() != "scrf":
+                spec_options = []
+                for o in options:
+                    print(o)
+                    if self.calc.type == CalcType.TS and o in [
+                        "ts",
+                        "NoEigenTest",
+                        "CalcFC",
+                    ]:
+                        continue
+                    elif self.calc.type == CalcType.CONSTR_OPT and o == "modredundant":
+                        continue
+                    spec_options.append(o)
+                if len(spec_options) > 0:
+                    spec_option_str = ", ".join(spec_options)
+                    confirmed_spec = f"{cmd}({spec_option_str}) "
+                    if cmd in self.KEYWORD_LIST:
+                        self.confirmed_specifications = (
+                            confirmed_spec + self.confirmed_specifications
+                        )
+                    else:
+                        self.confirmed_specifications += confirmed_spec
+
             # This ensures that the command line follows this pattern:
             # CMD1 <CMD2> METHOD/BASIS_SET <ADDITIONAL_OPTION1> ...
             if cmd in self.KEYWORD_LIST:
                 self.command_line = cmd_formatted + self.command_line
             else:
                 self.command_line = self.command_line + cmd_formatted
-                if cmd.lower() != "scrf":
-                    self.confirmed_specifications += cmd_formatted
 
         self.confirmed_specifications = self.confirmed_specifications.strip()
 

ccinput/tests/test_gaussian.py

@@ -1978,6 +1978,68 @@ def test_global_specification(self):
         self.assertTrue(self.is_equivalent(REF, inp.input_file))
         self.assertEqual(inp.confirmed_specifications.strip(), "scf(tight)")
 
+    def test_confirmed_command_specification(self):
+        params = {
+            "nproc": 8,
+            "mem": "10000MB",
+            "type": "Geometrical Optimisation",
+            "file": "Cl.xyz",
+            "software": "Gaussian",
+            "method": "M06-2X",
+            "basis_set": "Def2-SVP",
+            "charge": "-1",
+            "specifications": "opt(maxstep=5)",
+        }
+
+        inp = self.generate_calculation(**params)
+
+        REF = """
+        %chk=calc.chk
+        %nproc=8
+        %mem=10000MB
+        #p opt(maxstep=5) M062X/Def2SVP
+
+        File created by ccinput
+
+        -1 1
+        Cl 0.0 0.0 0.0
+
+        """
+
+        self.assertTrue(self.is_equivalent(REF, inp.input_file))
+        self.assertEqual(inp.confirmed_specifications.strip(), "opt(maxstep=5)")
+
+    def test_confirmed_command_specification_selective(self):
+        params = {
+            "nproc": 8,
+            "mem": "10000MB",
+            "type": "TS Optimisation",
+            "file": "Cl.xyz",
+            "software": "Gaussian",
+            "method": "M06-2X",
+            "basis_set": "Def2-SVP",
+            "charge": "-1",
+            "specifications": "opt(maxstep=5)",
+        }
+
+        inp = self.generate_calculation(**params)
+
+        REF = """
+        %chk=calc.chk
+        %nproc=8
+        %mem=10000MB
+        #p opt(maxstep=5, ts, NoEigenTest, CalcFC) M062X/Def2SVP
+
+        File created by ccinput
+
+        -1 1
+        Cl 0.0 0.0 0.0
+
+        """
+
+        self.assertTrue(self.is_equivalent(REF, inp.input_file))
+        self.assertEqual(inp.confirmed_specifications.strip(), "opt(maxstep=5)")
+
     def test_multiple_global_specification(self):
         params = {
             "nproc": 8,