add option to write eigenvectors and extra info in bands, useful for …

…visualisation, but we end up with bigger files

README.md

@@ -204,15 +204,22 @@ Calculate phonons with a 2x2x2 supercell, after geometry optimization (using the
 janus phonons --struct tests/data/NaCl.cif --supercell 2x2x2 --minimize --arch mace_mp --calc-kwargs "{'model' : 'small'}"
 ```
 
-This will save the Phonopy parameters, including displacements and force constants, to `NaCl-params.yml`, and the calculated band structure to `NaCl-auto-band.yml`, in addition to generating a log file, `phonons.log`, and summary of inputs, `phonons_summary.yml`.
+This will save the Phonopy parameters, including displacements and force constants, to `NaCl-phonopy.yml` and `NaCl-force\_constants.hdf5`, in addition to generating a log file, `phonons.log`, and summary of inputs, `phonons_summary.yml`.
+Additionaly, to calculate band structure and generate `NaCl-auto-bands.yml` use:
+
+```shell
+janus phonons --struct tests/data/NaCl.cif --supercell 2x2x2 --minimize --arch mace_mp --calc-kwargs "{'model' : 'small'}"
+```
+If you need eigenvectors and group velocities written add `--write-full` option. Will generate a much bigger bands file but can be
+used to visualise phonon modes.
 
 Further calculations, including thermal properties, DOS, and PDOS, can also be calculated (using a 2x3x4 supercell):
 
 ```shell
 janus phonons --struct tests/data/NaCl.cif --supercell 2x3x4 --dos --pdos --thermal --temp-start 0 --temp-end 300 --temp-step 50
 ```
 
-This will create additional output files: `NaCl-cv.dat` for the thermal properties (heat capacity, entropy, and free energy) between 0K and 300K, `NaCl-dos.dat` for the DOS, and `NaCl-pdos.dat` for the PDOS.
+This will create additional output files: `NaCl-thermal.dat` for the thermal properties (heat capacity, entropy, and free energy) between 0K and 300K, `NaCl-dos.dat` for the DOS, and `NaCl-pdos.dat` for the PDOS.
 
 For all options, run `janus phonons --help`.
 

janus_core/calculations/phonons.py

@@ -44,8 +44,11 @@ class Phonons:  # pylint: disable=too-many-instance-attributes
         Whether to plot various graphs as band stuctures, dos/pdos in svg.
         Default is False.
     symmetrize : bool
-        Whether to symmetrize force constants after cauclation.
+        Whether to symmetrize force constants after calculation.
         Default is False.
+    write_full : bool
+        Whether to maximize information written in various output files.
+        Default is True.
     minimize_kwargs : Optional[dict[str, Any]]
         Keyword arguments to pass to geometry optimizer. Default is {}.
     file_prefix : Optional[PathLike]
@@ -65,6 +68,7 @@ class Phonons:  # pylint: disable=too-many-instance-attributes
     """
 
     def __init__(  # pylint: disable=too-many-arguments
+        # pylint: disable=too-many-locals
         self,
         struct: Atoms,
         struct_name: Optional[str] = None,
@@ -77,6 +81,7 @@ def __init__(  # pylint: disable=too-many-arguments
         hdf5: bool = True,
         plot_to_file: bool = False,
         symmetrize: bool = False,
+        write_full: bool = True,
         minimize_kwargs: Optional[dict[str, Any]] = None,
         file_prefix: Optional[PathLike] = None,
         log_kwargs: Optional[dict[str, Any]] = None,
@@ -110,8 +115,11 @@ def __init__(  # pylint: disable=too-many-arguments
             Whether to plot various graphs as band stuctures, dos/pdos in svg.
             Default is False.
         symmetrize : bool
-            Whether to symmetrize force constants after cauclation.
+            Whether to symmetrize force constants after calculations.
             Default is False.
+        write_full : bool
+            Whether to maximize information written in various output files.
+            Default is True.
         minimize_kwargs : Optional[dict[str, Any]]
             Keyword arguments to pass to geometry optimizer. Default is {}.
         file_prefix : Optional[PathLike]
@@ -149,6 +157,7 @@ def __init__(  # pylint: disable=too-many-arguments
         self.hdf5 = hdf5
         self.plot_to_file = plot_to_file
         self.symmetrize = symmetrize
+        self.write_full = write_full
 
         if not self.struct.calc:
             raise ValueError("Please attach a calculator to `struct`.")
@@ -265,7 +274,10 @@ def write_band_structure(
 
         bands_file = self._set_filename("auto_bands.yml", bands_file)
         self.results["phonon"].auto_band_structure(
-            write_yaml=write_bands, filename=bands_file
+            write_yaml=write_bands,
+            filename=bands_file,
+            with_eigenvectors=self.write_full,
+            with_group_velocities=self.write_full,
         )
         if self.plot_to_file:
             bplt = self.results["phonon"].plot_band_structure()

janus_core/cli/phonons.py

@@ -96,6 +96,17 @@ def phonons(
     symmetrize: Annotated[
         bool, Option(help="Whether to symmetrize force constants.")
     ] = False,
+    write_full: Annotated[
+        bool,
+        Option(
+            help=(
+                """
+            Whether to maximize the amount of information written
+            in various output files.
+                  """
+            ),
+        ),
+    ] = True,
     fmax: Annotated[
         float, Option(help="Maximum force for optimization convergence.")
     ] = 0.1,
@@ -160,6 +171,9 @@ def phonons(
         Whether to minimize structure before calculations. Default is False.
     symmetrize : bool
         Whether to symmetrize force constants. Default is False.
+    write_full : bool
+        Whether to maximize information written in various output files.
+        Default is True.
     fmax : float
         Set force convergence criteria for optimizer in units eV/Å.
         Default is 0.1.
@@ -235,8 +249,9 @@ def phonons(
         "file_prefix": file_prefix,
         "log_kwargs": log_kwargs,
         "hdf5": hdf5,
-        "symmetrize": symmetrize,
         "plot_to_file": plot_to_file,
+        "symmetrize": symmetrize,
+        "write_full": write_full,
     }
 
     # Store inputs for yaml summary

tests/test_phonons_cli.py

@@ -20,8 +20,8 @@ def test_help():
     assert "Usage: janus phonons [OPTIONS]" in result.stdout
 
 
-def test_phonons(tmp_path):
-    """Test calculating phonons."""
+def test_bands(tmp_path):
+    """Test calculating force constants and bands."""
     log_path = tmp_path / "test.log"
     summary_path = tmp_path / "summary.yml"
     phonon_results = tmp_path / "NaCl-phonopy.yml"
@@ -46,6 +46,34 @@ def test_phonons(tmp_path):
     assert autoband_results.exists()
 
 
+def test_bands_simple(tmp_path):
+    """Test calculating force constants and reduced bands information."""
+    log_path = tmp_path / "test.log"
+    summary_path = tmp_path / "summary.yml"
+    autoband_results = tmp_path / "NaCl-auto_bands.yml"
+    result = runner.invoke(
+        app,
+        [
+            "phonons",
+            "--struct",
+            DATA_PATH / "NaCl.cif",
+            "--file-prefix",
+            tmp_path / "NaCl",
+            "--log",
+            log_path,
+            "--summary",
+            summary_path,
+            "--band",
+            "--no-write-full",
+        ],
+    )
+    assert result.exit_code == 0
+    assert autoband_results.exists()
+    with open(autoband_results, encoding="utf8") as file:
+        bands = yaml.safe_load(file)
+        assert "eigenvector" not in bands["phonon"][0]["band"][0].keys()
+
+
 def test_hdf5(tmp_path):
     """Test calculating phonons."""
     log_path = tmp_path / "test.log"
@@ -184,6 +212,9 @@ def test_plot(tmp_path):
     assert autoband_results.exists()
     for svg in svgs:
         assert svg.exists()
+    with open(autoband_results, encoding="utf8") as file:
+        bands = yaml.safe_load(file)
+        assert "eigenvector" in bands["phonon"][0]["band"][0].keys()
 
 
 def test_supercell(tmp_path):