Adding EoS plotting (stfc#332)

* Add option to plot EoS

* Update gitignore

* Test plotting EoS

* Allow plot kwargs for EoS

.gitignore

@@ -18,6 +18,7 @@
 *.jpeg
 *.dot
 *.png
+*.svg
 ~*
 *~
 .project

janus_core/calculations/eos.py

@@ -74,6 +74,10 @@ class EoS(BaseCalculation):
     write_kwargs : Optional[OutputKwargs],
         Keyword arguments to pass to ase.io.write to save generated structures.
         Default is {}.
+    plot_to_file : bool
+        Whether to save plot equation of state to svg. Default is False.
+    plot_kwargs : Optional[dict[str, Any]]
+        Keyword arguments to pass to EquationOfState.plot. Default is {}.
     file_prefix : Optional[PathLike]
         Prefix for output filenames. Default is inferred from structure name, or
         chemical formula of the structure.
@@ -119,6 +123,8 @@ def __init__(
         write_results: bool = True,
         write_structures: bool = False,
         write_kwargs: Optional[OutputKwargs] = None,
+        plot_to_file: bool = False,
+        plot_kwargs: Optional[dict[str, Any]] = None,
         file_prefix: Optional[PathLike] = None,
     ) -> None:
         """
@@ -174,12 +180,16 @@ def __init__(
         write_kwargs : Optional[OutputKwargs],
             Keyword arguments to pass to ase.io.write to save generated structures.
             Default is {}.
+        plot_to_file : bool
+            Whether to save plot equation of state to svg. Default is False.
+        plot_kwargs : Optional[dict[str, Any]]
+            Keyword arguments to pass to EquationOfState.plot. Default is {}.
         file_prefix : Optional[PathLike]
             Prefix for output filenames. Default is inferred from structure name, or
             chemical formula of the structure.
         """
-        (read_kwargs, minimize_kwargs, write_kwargs) = none_to_dict(
-            (read_kwargs, minimize_kwargs, write_kwargs)
+        (read_kwargs, minimize_kwargs, write_kwargs, plot_kwargs) = none_to_dict(
+            (read_kwargs, minimize_kwargs, write_kwargs, plot_kwargs)
         )
 
         self.min_volume = min_volume
@@ -192,6 +202,8 @@ def __init__(
         self.write_results = write_results
         self.write_structures = write_structures
         self.write_kwargs = write_kwargs
+        self.plot_to_file = plot_to_file
+        self.plot_kwargs = plot_kwargs
 
         if (
             (self.minimize or self.minimize_all)
@@ -243,12 +255,17 @@ def __init__(
                 "filemode": "a",
             }
 
-        # Set output file
+        # Set output files
         self.write_kwargs.setdefault("filename", None)
         self.write_kwargs["filename"] = self._build_filename(
             "generated.extxyz", filename=self.write_kwargs["filename"]
         ).absolute()
 
+        self.plot_kwargs.setdefault("filename", None)
+        self.plot_kwargs["filename"] = self._build_filename(
+            "eos-plot.svg", filename=self.plot_kwargs["filename"]
+        ).absolute()
+
         self.results = {}
         self.volumes = []
         self.energies = []
@@ -320,6 +337,9 @@ def run(self) -> EoSResults:
             "v_0": v_0,
         }
 
+        if self.plot_to_file:
+            eos.plot(**self.plot_kwargs)
+
         return self.results
 
     def _calc_volumes_energies(self) -> None:

janus_core/cli/eos.py

@@ -51,6 +51,10 @@ def eos(
         Option(help="Whether to write out all genereated structures."),
     ] = False,
     write_kwargs: WriteKwargs = None,
+    plot_to_file: Annotated[
+        bool,
+        Option(help="Whether to plot equation of state."),
+    ] = False,
     arch: Architecture = "mace_mp",
     device: Device = "cpu",
     model_path: ModelPath = None,
@@ -101,6 +105,8 @@ def eos(
     write_kwargs : Optional[dict[str, Any]],
         Keyword arguments to pass to ase.io.write to save generated structures.
         Default is {}.
+    plot_to_file : bool
+        Whether to save plot equation of state to svg. Default is False.
     arch : Optional[str]
         MLIP architecture to use for geometry optimization.
         Default is "mace_mp".
@@ -177,6 +183,7 @@ def eos(
         "minimize_kwargs": minimize_kwargs,
         "write_structures": write_structures,
         "write_kwargs": write_kwargs,
+        "plot_to_file": plot_to_file,
         "file_prefix": file_prefix,
     }
 

tests/test_eos.py

@@ -132,3 +132,21 @@ def test_logging(tmp_path):
 
     assert log_file.exists()
     assert single_point.struct.info["emissions"] > 0
+
+
+def test_plot(tmp_path):
+    """Test plotting equation of state."""
+    plot_file = tmp_path / "plot.svg"
+
+    eos = EoS(
+        struct_path=DATA_PATH / "NaCl.cif",
+        arch="mace_mp",
+        calc_kwargs={"model": MODEL_PATH},
+        plot_to_file=True,
+        plot_kwargs={"filename": plot_file},
+        file_prefix=tmp_path / "NaCl",
+    )
+
+    results = eos.run()
+    assert all(key in results for key in ("eos", "bulk_modulus", "e_0", "v_0"))
+    assert plot_file.exists()

tests/test_eos_cli.py

@@ -278,3 +278,25 @@ def test_invalid_traj_input(tmp_path):
     )
     assert result.exit_code == 1
     assert isinstance(result.exception, ValueError)
+
+
+def test_plot(tmp_path):
+    """Test plotting equation of state."""
+    file_prefix = tmp_path / "NaCl"
+    plot_path = tmp_path / "NaCl-eos-plot.svg"
+
+    result = runner.invoke(
+        app,
+        [
+            "eos",
+            "--struct",
+            DATA_PATH / "NaCl.cif",
+            "--n-volumes",
+            4,
+            "--plot-to-file",
+            "--file-prefix",
+            file_prefix,
+        ],
+    )
+    assert result.exit_code == 0
+    assert plot_path.exists()