add multi-isotope configuration support in FitOptions and InpManager

Author: KedoKudo

src/pleiades/sammy/fitting/options.py

@@ -223,6 +223,41 @@ def from_fitting_config(cls) -> "FitOptions":
 
         return options
 
+    @classmethod
+    def from_multi_isotope_config(cls) -> "FitOptions":
+        """Create a FitOptions instance configured for multi-isotope JSON mode fitting.
+
+        Multi-isotope mode combines ENDF extraction and Bayesian fitting in a single step
+        using JSON configuration files for multiple isotopes.
+
+        Key features for multi-isotope mode:
+        - UID 15: INPUT IS ENDF/B FILE (for JSON mode processing)
+        - UID 16: USE ENERGY RANGE FROM ENDF FILE (from ENDF data)
+        - UID 34: USE TWENTY SIGNIFICANT digits (for data format)
+        - UID 60: BROADENING IS WANTED (for instrumental broadening)
+        - UID 102: SOLVE BAYES EQUATIONS (fitting enabled)
+        - UID 133: CHI SQUARED IS WANTED (for fit quality)
+
+        Returns:
+            FitOptions: Instance configured for multi-isotope JSON mode fitting
+        """
+        # Create with default options
+        options = cls()
+
+        # Configure for multi-isotope JSON mode
+        options.endf = ENDFOptions(
+            input_is_endf_file_2=True,  # Enable JSON mode ENDF processing
+            use_energy_range_from_endf_file_2=True,  # Use ENDF energy range
+        )
+        options.experimental_data = ExperimentalDataInputOptions(
+            use_twenty_significant_digits=True  # Use twenty format
+        )
+        options.broadening = BroadeningOptions(broadening_is_wanted=True)
+        options.bayes_solution = BayesSolutionOptions(solve_bayes_equations=True)
+        options.lpt_output = LPTOutputOptions(chi_squared_is_wanted=True)
+
+        return options
+
     @classmethod
     def from_custom_config(cls, **kwargs) -> "FitOptions":
         """Create a FitOptions instance with custom settings.

src/pleiades/sammy/io/inp_manager.py

@@ -198,3 +198,23 @@ def create_fitting_inp(cls, output_path: Path, title: str = None) -> Path:
         options = FitOptions.from_fitting_config()
         manager = cls(options, title=title or "Bayesian fitting mode")
         return manager.write_inp_file(output_path)
+
+    @classmethod
+    def create_multi_isotope_inp(cls, output_path: Path, title: str = None, material_properties: Dict = None) -> Path:
+        """
+        Create input file for multi-isotope JSON mode fitting.
+
+        This method generates a complete INP file for multi-isotope fitting that includes
+        both static alphanumeric commands and calculated parameter sections.
+
+        Args:
+            output_path: Path to write the input file
+            title: Optional title for the inp file
+            material_properties: Optional dict with material properties for parameter calculations
+
+        Returns:
+            Path: Path to the created file
+        """
+        options = FitOptions.from_multi_isotope_config()
+        manager = cls(options, title=title or "Multi-isotope JSON mode fitting", reaction_type="transmission")
+        return manager.write_inp_file(output_path)

tests/unit/pleiades/sammy/fitting/test_fit_options.py

@@ -147,6 +147,28 @@ def test_from_custom_config():
     assert "DO NOT SOLVE BAYES EQUATIONS" in commands
 
 
+def test_from_multi_isotope_config():
+    """Test the factory method that creates FitOptions for multi-isotope JSON mode fitting."""
+    fit_options = FitOptions.from_multi_isotope_config()
+
+    # Verify multi-isotope mode settings
+    assert fit_options.endf.input_is_endf_file_2 is True
+    assert fit_options.endf.use_energy_range_from_endf_file_2 is True
+    assert fit_options.experimental_data.use_twenty_significant_digits is True
+    assert fit_options.broadening.broadening_is_wanted is True
+    assert fit_options.bayes_solution.solve_bayes_equations is True
+    assert fit_options.lpt_output.chi_squared_is_wanted is True
+
+    # Check generated commands for multi-isotope mode
+    commands = fit_options.get_alphanumeric_commands()
+    assert "INPUT IS ENDF/B FILE 2" in commands
+    assert "USE ENERGY RANGE FROM ENDF/B FILE 2" in commands
+    assert "USE TWENTY SIGNIFICANT DIGITS" in commands
+    assert "BROADENING IS WANTED" in commands
+    assert "SOLVE BAYES EQUATIONS" in commands
+    assert "CHI SQUARED IS WANTED" in commands
+
+
 def test_mutually_exclusive_options():
     """Test that mutually exclusive options are handled correctly."""
     # Create RMatrixOptions with mutually exclusive options

tests/unit/pleiades/sammy/io/test_inp_manager.py

@@ -242,3 +242,70 @@ def test_custom_inp_creation(temp_dir):
 
     assert isinstance(content, str)
     assert len(content) > 0  # Ensure some content was written
+
+
+def test_create_multi_isotope_inp(temp_dir):
+    """Test creating input file for multi-isotope JSON mode using class method."""
+    output_path = temp_dir / "multi_isotope.inp"
+
+    with patch.object(FitOptions, "from_multi_isotope_config") as mock_from_multi:
+        mock_options = MagicMock(spec=FitOptions)
+        mock_options.get_alphanumeric_commands.return_value = [
+            "INPUT IS ENDF/B FILE 2",
+            "USE ENERGY RANGE FROM ENDF/B FILE 2",
+            "USE TWENTY SIGNIFICANT DIGITS",
+            "BROADENING IS WANTED",
+            "SOLVE BAYES EQUATIONS",
+            "CHI SQUARED IS WANTED",
+        ]
+        mock_from_multi.return_value = mock_options
+
+        result_path = InpManager.create_multi_isotope_inp(output_path, title="Multi-isotope test")
+
+        assert result_path == output_path
+        assert output_path.exists()
+
+        with open(output_path, "r") as f:
+            content = f.read()
+
+        assert "Multi-isotope test" in content
+        assert "transmission" in content  # Reaction type should be set
+        assert "INPUT IS ENDF/B FILE 2" in content
+        assert "USE TWENTY SIGNIFICANT DIGITS" in content
+        assert "BROADENING IS WANTED" in content
+        mock_from_multi.assert_called_once()
+
+
+def test_multi_isotope_config_integration(temp_dir):
+    """Test multi-isotope configuration integration without mocking."""
+    output_path = temp_dir / "multi_isotope_real.inp"
+
+    # Test real implementation without mocking
+    result_path = InpManager.create_multi_isotope_inp(output_path, title="Real multi-isotope integration test")
+
+    assert result_path == output_path
+    assert output_path.exists()
+
+    with open(output_path, "r") as f:
+        content = f.read()
+
+    # Check for key multi-isotope commands
+    expected_commands = [
+        "INPUT IS ENDF/B FILE",
+        "USE ENERGY RANGE FROM ENDF",
+        "USE TWENTY SIGNIFICANT DIGITS",
+        "BROADENING IS WANTED",
+        "SOLVE BAYES EQUATIONS",
+        "CHI SQUARED IS WANTED",
+        "transmission",
+    ]
+
+    found_commands = []
+    for cmd in expected_commands:
+        if cmd in content:
+            found_commands.append(cmd)
+
+    # Should find most of the expected commands
+    assert (
+        len(found_commands) >= 6
+    ), f"Found only {len(found_commands)}/{len(expected_commands)} commands: {found_commands}"